opsecsystems commited on
Commit
d43787f
·
verified ·
1 Parent(s): 90ce774

Scripts of 2026-09-27: 2 new block(s), 545 manifest(s), 0 removed (part 3)

Browse files
Files changed (49) hide show
  1. manifests/eb/zenodo__6622367.json +21 -0
  2. manifests/ec/github.com__google__neuroglancer.json +0 -0
  3. manifests/ec/zenodo__20072888.json +75 -0
  4. manifests/ed/github.com__broadinstitute__tangram.json +210 -0
  5. manifests/ed/github.com__mindspacelab__aperiodic_test_retest_5year.json +84 -0
  6. manifests/ed/zenodo__20671852.json +201 -0
  7. manifests/ef/github.com__laboratory-of-vincent-breton-provencher__bouchardetal_2026.json +165 -0
  8. manifests/ef/github.com__pearlryder__subcellular-distribution-pipeline.json +255 -0
  9. manifests/ef/github.com__rishigami__swin-transformer-tf.json +48 -0
  10. manifests/ef/zenodo__20041637.json +39 -0
  11. manifests/ef/zenodo__20835637.json +84 -0
  12. manifests/f0/github.com__pgmpy__pgmpy.json +0 -0
  13. manifests/f0/github.com__scikit-fmm__scikit-fmm.json +237 -0
  14. manifests/f0/zenodo__21076315.json +48 -0
  15. manifests/f1/github.com__hakyimlab__metaxcan.json +1047 -0
  16. manifests/f2/github.com__nicalab__support.json +147 -0
  17. manifests/f2/zenodo__14254094.json +129 -0
  18. manifests/f2/zenodo__19331923.json +192 -0
  19. manifests/f3/github.com__dicemt__dti-noddi.json +57 -0
  20. manifests/f3/zenodo__15095228.json +111 -0
  21. manifests/f5/github.com__jlhos-fmri__clinicalfrequencyanalysistoolkit.json +228 -0
  22. manifests/f5/zenodo__8018820.json +1002 -0
  23. manifests/f6/figshare__29941784.json +84 -0
  24. manifests/f6/github.com__fraunhoferchalmerscentre__neuralodepopulation.json +111 -0
  25. manifests/f6/github.com__oranges7__vcboost.json +165 -0
  26. manifests/f7/github.com__a96123155__utr-lm.json +102 -0
  27. manifests/f7/github.com__iamnielsjanssen__display_melodics.json +39 -0
  28. manifests/f7/github.com__kpm-floesch__nicetfrplot.json +39 -0
  29. manifests/f7/github.com__oxpig__calm.json +165 -0
  30. manifests/f7/zenodo__21207822.json +156 -0
  31. manifests/f8/github.com__precimed__gsa-mixer.json +948 -0
  32. manifests/f8/github.com__thuretlabkcl__tnf-scrnaseq-neurogenesis.json +84 -0
  33. manifests/f9/github.com__jacobgil__pytorch-grad-cam.json +534 -0
  34. manifests/f9/zenodo__18508813.json +30 -0
  35. manifests/fa/github.com__infectionmedicineproteomics__binn.json +192 -0
  36. manifests/fa/github.com__nicalab__graphycs.json +138 -0
  37. manifests/fa/github.com__shekharlab__amacrinecells.json +246 -0
  38. manifests/fa/zenodo__18791231.json +210 -0
  39. manifests/fb/github.com__bruce-ywj__ernie-rna.json +165 -0
  40. manifests/fb/github.com__kr-colab__popgen-npe.json +588 -0
  41. manifests/fc/github.com__mmtrebuchet__bpreveal.json +732 -0
  42. manifests/fc/github.com__zhou-1314__garfield-reproducibility.json +552 -0
  43. manifests/fc/zenodo__21730421.json +264 -0
  44. manifests/fd/github.com__nagellab__mayetal2026.json +0 -0
  45. manifests/fe/github.com__scverse__scvi-tools.json +3072 -0
  46. manifests/fe/github.com__yingqihao2022__panda.json +75 -0
  47. manifests/fe/zenodo__16809359.json +255 -0
  48. manifests/ff/github.com__precimed__python_convert.json +309 -0
  49. manifests/ff/zenodo__19471544.json +543 -0
manifests/eb/zenodo__6622367.json ADDED
@@ -0,0 +1,21 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:6622367",
4
+ "url": "10.5281/zenodo.6622367",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "CC-BY-4.0",
8
+ "license_confirmed_by": "license of the archive's record",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "readme.txt",
13
+ "sha256": "43fd78d03df9f02e77725a85a27a73264151026283a7f9b34805c6c4303819da",
14
+ "language": "Text",
15
+ "lines": 78,
16
+ "truncated": false,
17
+ "block": 4,
18
+ "row": 2458
19
+ }
20
+ ]
21
+ }
manifests/ec/github.com__google__neuroglancer.json ADDED
The diff for this file is too large to render. See raw diff
 
manifests/ec/zenodo__20072888.json ADDED
@@ -0,0 +1,75 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:20072888",
4
+ "url": "10.5281/zenodo.20072888",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "Apache-2.0",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "610a07a15c8ba36b52df02f5d15083c0d3ed2bf859216076a476b9a15d8cdffb",
14
+ "language": "License",
15
+ "lines": 102,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8136
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "5e7f865aa19bc46d3d14362325bc3eaac25ca9dd7a9356cb9d70ee11783962de",
23
+ "language": "Text",
24
+ "lines": 99,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2539
28
+ },
29
+ {
30
+ "path": "evaluation.py",
31
+ "sha256": "b3846507da2e620f8e17014a1c042b3092e3d93b71bb7ab5c8a5630d314d7f40",
32
+ "language": "Python",
33
+ "lines": 281,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 24978
37
+ },
38
+ {
39
+ "path": "model.py",
40
+ "sha256": "24f2ee742e965c91e1b49b4f9e257cebd79239719ef71300d3855b0c9f667120",
41
+ "language": "Python",
42
+ "lines": 300,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 25094
46
+ },
47
+ {
48
+ "path": "model_eval.py",
49
+ "sha256": "b73f25cab6467b369e69a71c164f02095e5cfe0a2a6e8bb38fb0cc3fc9788391",
50
+ "language": "Python",
51
+ "lines": 151,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 22890
55
+ },
56
+ {
57
+ "path": "train.py",
58
+ "sha256": "21ea48e33f2b4d953bd73130d82fceaf4d847ccfa5cd8d6c7420ecc5ef88fd93",
59
+ "language": "Python",
60
+ "lines": 133,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 21930
64
+ },
65
+ {
66
+ "path": "utils.py",
67
+ "sha256": "4c4914be86fa0bf29f8cbe0a8451ae2c7b5bdfe35360642a21e7cffd9dde899d",
68
+ "language": "Python",
69
+ "lines": 93,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 21243
73
+ }
74
+ ]
75
+ }
manifests/ed/github.com__broadinstitute__tangram.json ADDED
@@ -0,0 +1,210 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/broadinstitute/tangram",
4
+ "url": "https://github.com/broadinstitute/Tangram",
5
+ "host": "github.com",
6
+ "commit": "4c68995a418f41dc8caef567598c4d9b47781a13",
7
+ "license": "BSD-3-Clause",
8
+ "license_confirmed_by": "license file LICENSE.md",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE.md",
13
+ "sha256": "576da33f78a74fe966fdda80b6f8aaa2eafdc2ff0dd856b393e37f5ade1a98f6",
14
+ "language": "License",
15
+ "lines": 29,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8117
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "e39f004fac1efc7b94c9e9aea9c5f52cb884606e38c4797d6563f72ea7f36dbc",
23
+ "language": "Text",
24
+ "lines": 170,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2649
28
+ },
29
+ {
30
+ "path": "cell_selection/__init__.py",
31
+ "sha256": "f0f6bc38a78af01b60d99a69ed5bdb84ce8a4a92cc979ce633bc59d04e6e7435",
32
+ "language": "Python",
33
+ "lines": 1,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 17369
37
+ },
38
+ {
39
+ "path": "cell_selection/cell_sampling.py",
40
+ "sha256": "f83d9f82e8f2af9afdee473bc7ed4d1a9300dd0efe05756e49fcb13986da439d",
41
+ "language": "Python",
42
+ "lines": 44,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 20275
46
+ },
47
+ {
48
+ "path": "docs/source/conf.py",
49
+ "sha256": "88956deb066cceddec6773ca240cc49a3eb5ac3761a841238cab0b122b51dc0c",
50
+ "language": "Python",
51
+ "lines": 70,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 20852
55
+ },
56
+ {
57
+ "path": "gene_selection/__init__.py",
58
+ "sha256": "b646a3476eeb40fd354551123602f7f2c9ca26417c6c1fdd09b1f05ceb6a190c",
59
+ "language": "Python",
60
+ "lines": 4,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 17626
64
+ },
65
+ {
66
+ "path": "gene_selection/celltype_specific_genes.py",
67
+ "sha256": "eba8feddb9e858eb4ded654bf303de484c9732b2a58ebff179828365b80e2d58",
68
+ "language": "Python",
69
+ "lines": 12,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 18084
73
+ },
74
+ {
75
+ "path": "gene_selection/highly_variable_genes.py",
76
+ "sha256": "a3a16ed5aa65a9a9032fc1bdbdaecc02ab70a30bdbd79822c161119e2a81951a",
77
+ "language": "Python",
78
+ "lines": 9,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 17716
82
+ },
83
+ {
84
+ "path": "gene_selection/spapros_genes.py",
85
+ "sha256": "b3886326b6cbcfd665f9e740e93706de9db351d4d808063950de4a803eea48b6",
86
+ "language": "Python",
87
+ "lines": 13,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 17862
91
+ },
92
+ {
93
+ "path": "gene_selection/spatially_variable_genes.py",
94
+ "sha256": "b4d498c783903abb78386775a63b6f420ce2aef4feac3da79929193c88c81908",
95
+ "language": "Python",
96
+ "lines": 13,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 17845
100
+ },
101
+ {
102
+ "path": "setup.py",
103
+ "sha256": "758bf285b004fc6cd047cacf4e741c5325eb88f40377792ff7f593f2fbb70953",
104
+ "language": "Python",
105
+ "lines": 37,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 18957
109
+ },
110
+ {
111
+ "path": "tangram/__init__.py",
112
+ "sha256": "c01b2b1a2faa95b40c9c61ab9ff63881a8e4b8b86c11df4b66983be3ed1f1edc",
113
+ "language": "Python",
114
+ "lines": 5,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 17667
118
+ },
119
+ {
120
+ "path": "tangram/_version.py",
121
+ "sha256": "6b0cdd3e99141c22071f64c23a24084f04f900ef010206bf1c1e5d99ea189eb9",
122
+ "language": "Python",
123
+ "lines": 3,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 17380
127
+ },
128
+ {
129
+ "path": "tangram/mapping_optimizer.py",
130
+ "sha256": "eb6837258289f97919b7b7f597a20d1ffc984a71baa96d60bee5eb1445eebcf1",
131
+ "language": "Python",
132
+ "lines": 639,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 27491
136
+ },
137
+ {
138
+ "path": "tangram/mapping_parameter_tuning.py",
139
+ "sha256": "9ef409cf2f815e2fc6fed6215c66cbb27ab1a1cdbd4de0ae5a32b3a24eeac119",
140
+ "language": "Python",
141
+ "lines": 272,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 25732
145
+ },
146
+ {
147
+ "path": "tangram/mapping_utils.py",
148
+ "sha256": "3aaddf186006bdeed336bb013a2bfc152417872c9e1ebd9b7480a7708bdacdd1",
149
+ "language": "Python",
150
+ "lines": 428,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 26861
154
+ },
155
+ {
156
+ "path": "tangram/plot_utils.py",
157
+ "sha256": "fd10fd5a9bee359797a54ca4d353c27515648b3caa58486b45d3a40ba32bf7a3",
158
+ "language": "Python",
159
+ "lines": 724,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 27347
163
+ },
164
+ {
165
+ "path": "tangram/spatial_weights.py",
166
+ "sha256": "4d09a9e2d9d7bb04918f32c6ace625d83b251273f04766e7490014d7a7915c4b",
167
+ "language": "Python",
168
+ "lines": 30,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 19295
172
+ },
173
+ {
174
+ "path": "tangram/utils.py",
175
+ "sha256": "e40316bea7e486e5bfae431fdc1207e1e38ec6119c6ce3381df74f9e1a0907ac",
176
+ "language": "Python",
177
+ "lines": 842,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 27645
181
+ },
182
+ {
183
+ "path": "tests/tangram_test.py",
184
+ "sha256": "9c1b12388733bbc2d8df7abad40d9da9138058efa36f018ff57121d2b11404c7",
185
+ "language": "Python",
186
+ "lines": 217,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 23913
190
+ },
191
+ {
192
+ "path": "tutorial_tangram_with_squidpy.ipynb",
193
+ "sha256": "5b03822c525cd3a9f89adf25a86dfc0d30c1e9481bc7cb60c0bf5e0cdc5d4407",
194
+ "language": "Jupyter",
195
+ "lines": 456,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 7782
199
+ },
200
+ {
201
+ "path": "tutorial_tangram_without_squidpy.ipynb",
202
+ "sha256": "ea65a20a96b6dce17985a10ba6a146bb97dcc92345f349a1220986989a9da33f",
203
+ "language": "Jupyter",
204
+ "lines": 362,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 7744
208
+ }
209
+ ]
210
+ }
manifests/ed/github.com__mindspacelab__aperiodic_test_retest_5year.json ADDED
@@ -0,0 +1,84 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/mindspacelab/aperiodic_test_retest_5year",
4
+ "url": "https://github.com/MindSpaceLab/Aperiodic_Test_Retest_5year",
5
+ "host": "github.com",
6
+ "commit": "e056acf5244f1b0becfc82591736031431f59ab3",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "4c128caa0c82f71422fb5a1eb53649d5f5b40625c001f76de5a6a88212f0f76f",
14
+ "language": "License",
15
+ "lines": 21,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8006
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "c02fd3db11f1f9e484ea20fdd46f98fa73393c0d33f01c9b361f125ae5a9a6f5",
23
+ "language": "Text",
24
+ "lines": 20,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2354
28
+ },
29
+ {
30
+ "path": "notebooks/IfAdo_analyses.Rmd",
31
+ "sha256": "b822bbed44dda05a2d0a70e3070907e9a00bb4bc838b084dc2286267c5820f0f",
32
+ "language": "R",
33
+ "lines": 2077,
34
+ "truncated": false,
35
+ "block": 4,
36
+ "row": 1239
37
+ },
38
+ {
39
+ "path": "notebooks/IfAdo_preprocessing.ipynb",
40
+ "sha256": "d375a23856cf7936befe0cc694bce1c77dcd4e97342c1638629a6fca5708bd19",
41
+ "language": "Jupyter",
42
+ "lines": 1986,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 7896
46
+ },
47
+ {
48
+ "path": "src/__init__.py",
49
+ "sha256": "8bb7fe863f8e6093f89eadc245c68ad46da10f86dc228dfde2f3d1b129996c71",
50
+ "language": "Python",
51
+ "lines": 3,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 17435
55
+ },
56
+ {
57
+ "path": "src/preprocessing.py",
58
+ "sha256": "c3d010fc45f11704c8a2bfd0346273617142dba18b2fdc1639c3aa32321a545c",
59
+ "language": "Python",
60
+ "lines": 312,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 26175
64
+ },
65
+ {
66
+ "path": "src/utils.py",
67
+ "sha256": "ce2a6548fbe3ce8d5cbb31320e6bcdaca834fbe73b007385e71c1352e2083935",
68
+ "language": "Python",
69
+ "lines": 1086,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 27884
73
+ },
74
+ {
75
+ "path": "src/viz.py",
76
+ "sha256": "469dbe3a3f80a889382b960d01948c218843e913b32cfaf8eb5166b59e94366d",
77
+ "language": "Python",
78
+ "lines": 47,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 19800
82
+ }
83
+ ]
84
+ }
manifests/ed/zenodo__20671852.json ADDED
@@ -0,0 +1,201 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:20671852",
4
+ "url": "https://doi.org/10.5281/zenodo.20671852",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "CC-BY-4.0",
8
+ "license_confirmed_by": "license of the archive's record",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "2024-08-01_Zhaoetal2022Dev_CodeFor_SCTv5IntegrateSeuratV5.R",
13
+ "sha256": "a4d46c318342640403a39fa241f608a3bb3212b9758080215096b7cf8beb69e5",
14
+ "language": "R",
15
+ "lines": 385,
16
+ "truncated": false,
17
+ "block": 4,
18
+ "row": 1083
19
+ },
20
+ {
21
+ "path": "2024-08-15_Sox10Dom_GEMMA_GWAS_Aganglionosis_AllChrs_PrepPedFiles.R",
22
+ "sha256": "76f999d69b5b83e0c33bd0acda3c4ccba365c7d7bd906314a64c89651123b4c3",
23
+ "language": "R",
24
+ "lines": 454,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 1037
28
+ },
29
+ {
30
+ "path": "2024-08-15_Sox10Dom_GEMMA_GWAS_Aganglionosis_No5X15Chrs_PrepPedFiles.R",
31
+ "sha256": "a16a8ccdcfb9c82fa61e7ee71bd29c6e244b6a665aad987c8186fa4a242fa3ed",
32
+ "language": "R",
33
+ "lines": 435,
34
+ "truncated": false,
35
+ "block": 4,
36
+ "row": 1023
37
+ },
38
+ {
39
+ "path": "2024-08-19_Sox10Dom_GEMMA_GWAS_Aganglionosis_Sex-Specific_AllChrs_PrepPedFiles.R",
40
+ "sha256": "0e65173fbbca5dc9c146ec09e916f794bed8b0effa0285a484b7e5d9d2adffa4",
41
+ "language": "R",
42
+ "lines": 755,
43
+ "truncated": false,
44
+ "block": 4,
45
+ "row": 1116
46
+ },
47
+ {
48
+ "path": "2024-08-21_NeuralCrestSubset_Zhaoetal2022Dev_CodeFor_SCTv5IntegrateSeuratV5.R",
49
+ "sha256": "aca1f72fd30d53aa9f5afdfd4096dfb62d821c7cd0068e4156752e4f9b52022f",
50
+ "language": "R",
51
+ "lines": 269,
52
+ "truncated": false,
53
+ "block": 4,
54
+ "row": 952
55
+ },
56
+ {
57
+ "path": "2024-08-29_Sox10Dom_GEMMA_GWAS_Aganglionosis_AllChrs_PrepPedFiles_JEFFSMITH.R",
58
+ "sha256": "eff54c1cdc6292ab3f0258a281e2cc9079d2a7cd2c8d93158bffe83b0a2c032b",
59
+ "language": "R",
60
+ "lines": 190,
61
+ "truncated": false,
62
+ "block": 4,
63
+ "row": 864
64
+ },
65
+ {
66
+ "path": "2024-09-03_PlottingPedigreeMeasurementsPCALength.R",
67
+ "sha256": "4fbc95d9a4f81d9180403170bb1bb2d01b9467b07a909b16759b1f6c6bad28ab",
68
+ "language": "R",
69
+ "lines": 523,
70
+ "truncated": false,
71
+ "block": 4,
72
+ "row": 1111
73
+ },
74
+ {
75
+ "path": "2024-09-16_snATAC-seq_Phox2bH2B-CFP_16.6dpc_ImportProcessing.R",
76
+ "sha256": "573116c0e871929100ee15c98795367513cebad2b6ab52b2f33e1b72b74915d9",
77
+ "language": "R",
78
+ "lines": 1356,
79
+ "truncated": false,
80
+ "block": 4,
81
+ "row": 1222
82
+ },
83
+ {
84
+ "path": "2024-10-02_ModifierInterval_CandidateGenePipeline_Part2+3_V1.R",
85
+ "sha256": "8dc01c33d16db1b4c10c72325689b713069a2ab496213b6438a9c70373568921",
86
+ "language": "R",
87
+ "lines": 1878,
88
+ "truncated": false,
89
+ "block": 4,
90
+ "row": 1233
91
+ },
92
+ {
93
+ "path": "2024-10-03_ModifierInterval_CandidateGenePipeline_Part4_V2.R",
94
+ "sha256": "49a810ddf0cdbcb9a96be2dfbc2a8f9dbb8a91149c152db6cdeff9abfe1ff1db",
95
+ "language": "R",
96
+ "lines": 463,
97
+ "truncated": false,
98
+ "block": 4,
99
+ "row": 1105
100
+ },
101
+ {
102
+ "path": "2024-10-03_ModifierInterval_CandidateGenePipeline_Part5_V1.R",
103
+ "sha256": "ee0259c69bbcc3c296a96b9ea5e1b9ab4b12727965e53d9aa5537cb9d5cf4573",
104
+ "language": "R",
105
+ "lines": 494,
106
+ "truncated": false,
107
+ "block": 4,
108
+ "row": 1112
109
+ },
110
+ {
111
+ "path": "2024-10-04_ModifierInterval_CandidateGenePipeline_Part1_V3.R",
112
+ "sha256": "c5dbcf9e990e343c0d260cc8bf35f4796230072dc5d7d202c4bdf389a2cd9f63",
113
+ "language": "R",
114
+ "lines": 1094,
115
+ "truncated": false,
116
+ "block": 4,
117
+ "row": 1201
118
+ },
119
+ {
120
+ "path": "2024-10-08_ModifierInterval_CandidateGenePipeline_Part6_V1.R",
121
+ "sha256": "8fb9feb4ce7744581fef7f04bd9c439b7397d657dd801f0a3d3c14e306f2f088",
122
+ "language": "R",
123
+ "lines": 389,
124
+ "truncated": false,
125
+ "block": 4,
126
+ "row": 1081
127
+ },
128
+ {
129
+ "path": "2024-10-25_TelocytesExpression.R",
130
+ "sha256": "fd35d4ab8231bcebe7be0216ac9bc4c8cc0eccfd90a5814417ae62de0436d5eb",
131
+ "language": "R",
132
+ "lines": 212,
133
+ "truncated": false,
134
+ "block": 4,
135
+ "row": 916
136
+ },
137
+ {
138
+ "path": "2024-11-12_ModifierInterval_CandidateGenePipeline_SuppFigureforPart2+3.R",
139
+ "sha256": "aa5e2aeb0649786d02fddd568d3ff51ab3a4ba166e006be199aba596d628f9fc",
140
+ "language": "R",
141
+ "lines": 225,
142
+ "truncated": false,
143
+ "block": 4,
144
+ "row": 985
145
+ },
146
+ {
147
+ "path": "2024-11-13_ModifierInterval_CandidateGenePipeline_SuppFigureforPart5.R",
148
+ "sha256": "b945199f26d4c71d5ea0937e29ccfa610a2bcce0ec8144e146560d9f92626ef1",
149
+ "language": "R",
150
+ "lines": 69,
151
+ "truncated": false,
152
+ "block": 4,
153
+ "row": 460
154
+ },
155
+ {
156
+ "path": "2024-12-05_CandidateGenesComparisonsCrossModality.R",
157
+ "sha256": "f46bb570e6a62d9d3069bd39b55e715f5381cab4a2d940be7d6c66c692bef0de",
158
+ "language": "R",
159
+ "lines": 729,
160
+ "truncated": false,
161
+ "block": 4,
162
+ "row": 1169
163
+ },
164
+ {
165
+ "path": "2024-12-18_CandidateGenes_OverlapWithHumanGWASHit.R",
166
+ "sha256": "8cce0db1fc9a35a312be3d0e50c96e6d5084af0880b3472fbc2ba6bd29e03f24",
167
+ "language": "R",
168
+ "lines": 458,
169
+ "truncated": false,
170
+ "block": 4,
171
+ "row": 1125
172
+ },
173
+ {
174
+ "path": "2024-12-18_CandidateGenes_VariantsDifferentThanB6_FunctionalPrediction_V2.R",
175
+ "sha256": "e12e0849f5fa0bf4278d6655dc41807f5a2565953d7d41189b75fab65187a441",
176
+ "language": "R",
177
+ "lines": 556,
178
+ "truncated": false,
179
+ "block": 4,
180
+ "row": 1149
181
+ },
182
+ {
183
+ "path": "2024-12-26_CandidateGene_ExonPheWAS_ManhattanPlots.R",
184
+ "sha256": "26fd07247d9fbbddb69a47b34d0cf718ad309eb612baa74fce7051c6876f64b6",
185
+ "language": "R",
186
+ "lines": 221,
187
+ "truncated": false,
188
+ "block": 4,
189
+ "row": 941
190
+ },
191
+ {
192
+ "path": "2025-02-12_ModifierInterval_CandidateGenePipeline_Part7_V2.R",
193
+ "sha256": "1bfcd396fce8453b87420a7b69d87618ca6b7e4b9c40bcf27b7ede979b3270c8",
194
+ "language": "R",
195
+ "lines": 1092,
196
+ "truncated": false,
197
+ "block": 4,
198
+ "row": 1218
199
+ }
200
+ ]
201
+ }
manifests/ef/github.com__laboratory-of-vincent-breton-provencher__bouchardetal_2026.json ADDED
@@ -0,0 +1,165 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/laboratory-of-vincent-breton-provencher/bouchardetal_2026",
4
+ "url": "https://github.com/Laboratory-of-Vincent-Breton-Provencher/BouchardEtAl_2026/tree/v1.0.0",
5
+ "host": "github.com",
6
+ "commit": "df971002da47859d93ed7d7b1262b47f628252b7",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "Figure_1B.py",
13
+ "sha256": "a155c51ec2b9b825694fabf3c771ac1c0703cb424308b265bc64c4854358a0f5",
14
+ "language": "Python",
15
+ "lines": 197,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 23540
19
+ },
20
+ {
21
+ "path": "Figure_1FGH_2BCDE.py",
22
+ "sha256": "020253b344cdc48b649ddf3021d10246c5864807e96b2b9da5b3c08322478dac",
23
+ "language": "Python",
24
+ "lines": 454,
25
+ "truncated": false,
26
+ "block": 3,
27
+ "row": 26848
28
+ },
29
+ {
30
+ "path": "Figure_2A_S2D.py",
31
+ "sha256": "8b97b1d4289fb28a07c67ffbb5e8560fb657344ccf14af0d67d5123a746be312",
32
+ "language": "Python",
33
+ "lines": 266,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 25495
37
+ },
38
+ {
39
+ "path": "Figure_3B-H_S4ACDEFH.py",
40
+ "sha256": "30a038d21f9c8a1337f17734c32197b07de08b85342c87cc3258784b543f770d",
41
+ "language": "Python",
42
+ "lines": 735,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 27514
46
+ },
47
+ {
48
+ "path": "Figure_3IJ.py",
49
+ "sha256": "4b41092e7fa81e6384ffa19ddb8dddfd6861fdc33a1b6a67feb398e0286c6526",
50
+ "language": "Python",
51
+ "lines": 308,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 25619
55
+ },
56
+ {
57
+ "path": "Figure_4.py",
58
+ "sha256": "eec1eec2b5140df2dc07f062d8ffd0b75e4f831350457e240f2055f626bbdcc8",
59
+ "language": "Python",
60
+ "lines": 423,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 26612
64
+ },
65
+ {
66
+ "path": "Figure_5_S6.py",
67
+ "sha256": "e36a1920eaf679021794e1c51c4cc90318d3ac6cfb2a23e7aa1a7827683ac8a9",
68
+ "language": "Python",
69
+ "lines": 400,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 26686
73
+ },
74
+ {
75
+ "path": "Figure_S2B.py",
76
+ "sha256": "d4e66952b38440736f839621cf13165d3af71c805878f2fe15e98d601f789cca",
77
+ "language": "Python",
78
+ "lines": 90,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 21466
82
+ },
83
+ {
84
+ "path": "Figure_S2C_S5CD.py",
85
+ "sha256": "f104fadc0d259354158a7f5400c81270a2f867db7019955f4cacc0cc714f5b31",
86
+ "language": "Python",
87
+ "lines": 269,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 25409
91
+ },
92
+ {
93
+ "path": "Figure_S2EF.py",
94
+ "sha256": "b911cf2d04792eb0ad2c267493d669281b4fcf6d8d6577fc7ad8a3f868d234cf",
95
+ "language": "Python",
96
+ "lines": 264,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 25323
100
+ },
101
+ {
102
+ "path": "Figure_S2G.py",
103
+ "sha256": "6cf034909247709f57d868a7aafa804e19e76e88d4abe770831015f96d13e83c",
104
+ "language": "Python",
105
+ "lines": 155,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 23344
109
+ },
110
+ {
111
+ "path": "Figure_S3.py",
112
+ "sha256": "fadbb5a4c93be638309a3425518dc093f8c49a10776c70ff4f8b4e4e86c1f11f",
113
+ "language": "Python",
114
+ "lines": 473,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 26884
118
+ },
119
+ {
120
+ "path": "Figure_S4B.py",
121
+ "sha256": "dcf8ef1a82634b424f4b989184dda8ed2af3283cea463642612e6cc126ba0a3c",
122
+ "language": "Python",
123
+ "lines": 517,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 27115
127
+ },
128
+ {
129
+ "path": "Figure_S4I.py",
130
+ "sha256": "8a651c16ef9589993fb3c6edc2dcda9907a8263c0abedd2c0eeef2743c51929d",
131
+ "language": "Python",
132
+ "lines": 365,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 26339
136
+ },
137
+ {
138
+ "path": "Figure_S5EFG.py",
139
+ "sha256": "9057fea0e4bd10a255df1cbac7454756d2a5cb85efc80046fc429882548e836a",
140
+ "language": "Python",
141
+ "lines": 466,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 26767
145
+ },
146
+ {
147
+ "path": "LICENSE",
148
+ "sha256": "5a92ccf83ce11d1a87dde05956e55b4058088c5c26ac09697f5c20524a76443d",
149
+ "language": "License",
150
+ "lines": 21,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 8075
154
+ },
155
+ {
156
+ "path": "README.md",
157
+ "sha256": "496e24017d55b3a9702d0b861170cf41bce1647262e4aed1e7b43c3e6a27e6eb",
158
+ "language": "Text",
159
+ "lines": 86,
160
+ "truncated": false,
161
+ "block": 4,
162
+ "row": 2480
163
+ }
164
+ ]
165
+ }
manifests/ef/github.com__pearlryder__subcellular-distribution-pipeline.json ADDED
@@ -0,0 +1,255 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/pearlryder/subcellular-distribution-pipeline",
4
+ "url": "https://github.com/pearlryder/subcellular-distribution-pipeline/tree/v1.0.0",
5
+ "host": "github.com",
6
+ "commit": "414b5507455e316cabf67a99f47811113e7c25ea",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "894f6bfa27cd0265476bc595d20f10c1d2af8a18b373e51f12cac30ff4005107",
14
+ "language": "License",
15
+ "lines": 21,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 7963
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "ef3b2bea75531f3e65ba7373fddc4f3e75c59c79268712cf64103b1a2804fed2",
23
+ "language": "Text",
24
+ "lines": 7,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2310
28
+ },
29
+ {
30
+ "path": "init-tables.sh",
31
+ "sha256": "c93ab6110004bfb51827e12bde2cdde29ec0310184b5dedabacbf8406c497020",
32
+ "language": "Shell",
33
+ "lines": 5,
34
+ "truncated": false,
35
+ "block": 4,
36
+ "row": 1305
37
+ },
38
+ {
39
+ "path": "jupyter/notebooks/pipeline/pipeline.ipynb",
40
+ "sha256": "8ad15b5e516469d4cb9ec120dd504b7055375acf500f96332c60e5baba302572",
41
+ "language": "Jupyter",
42
+ "lines": 859,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 7820
46
+ },
47
+ {
48
+ "path": "jupyter/notebooks/pipeline/pipeline.py",
49
+ "sha256": "a24cd9ead45980272392e0f236b1489358aabb618d39aa31eed847cac2b352a0",
50
+ "language": "Python",
51
+ "lines": 854,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 27728
55
+ },
56
+ {
57
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/.ipynb_checkpoints/playground_Sec61b-checkpoint.ipynb",
58
+ "sha256": "39d11ab839236141f72cd133758a35a28901c6e450027756182bd8cae03bc2e6",
59
+ "language": "Jupyter",
60
+ "lines": 263,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 7548
64
+ },
65
+ {
66
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/.ipynb_checkpoints/playground_dots-checkpoint.ipynb",
67
+ "sha256": "1ee78c91c62fbef61d45cb3630f0641c2fcb647efd0e3eff6d1eac1566d15608",
68
+ "language": "Jupyter",
69
+ "lines": 261,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 7607
73
+ },
74
+ {
75
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/.ipynb_checkpoints/playground_filament3d-checkpoint.ipynb",
76
+ "sha256": "31b92fc79534f0947c4867fdb5b0b634c186a64f53e896a2d02fa3021677343a",
77
+ "language": "Jupyter",
78
+ "lines": 246,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 7554
82
+ },
83
+ {
84
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/.ipynb_checkpoints/playground_gja1-checkpoint.ipynb",
85
+ "sha256": "db676de5336c31dd340d0d831f1902af8fd2d7f82aee9490ca0abb4711c1e928",
86
+ "language": "Jupyter",
87
+ "lines": 230,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 7510
91
+ },
92
+ {
93
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/.ipynb_checkpoints/playground_spotty-checkpoint.ipynb",
94
+ "sha256": "149d3e33b1b077453054a464122113b287866eeb9a08ba53a149277d6613c1c0",
95
+ "language": "Jupyter",
96
+ "lines": 248,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 7505
100
+ },
101
+ {
102
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/.ipynb_checkpoints/playground_st6gal1-checkpoint.ipynb",
103
+ "sha256": "d7b1108e88487680497a9b100ee527501cfcbf8c3c29e3061d72df27bcd2a4e9",
104
+ "language": "Jupyter",
105
+ "lines": 297,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 7620
109
+ },
110
+ {
111
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/playground_Sec61_dual.ipynb",
112
+ "sha256": "04d7a5353ff674514c0cbc9a17ffbf309cfe48d8db56666f75715d3bdfdea368",
113
+ "language": "Jupyter",
114
+ "lines": 247,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 7525
118
+ },
119
+ {
120
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/playground_Sec61b.ipynb",
121
+ "sha256": "39d11ab839236141f72cd133758a35a28901c6e450027756182bd8cae03bc2e6",
122
+ "language": "Jupyter",
123
+ "lines": 263,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 7548
127
+ },
128
+ {
129
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/playground_curvi.ipynb",
130
+ "sha256": "6304f6149a896cebc01d681c89b4d3e722a8b566053c6dbefce2cf2b16029d22",
131
+ "language": "Jupyter",
132
+ "lines": 240,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 7533
136
+ },
137
+ {
138
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/playground_dots.ipynb",
139
+ "sha256": "1ee78c91c62fbef61d45cb3630f0641c2fcb647efd0e3eff6d1eac1566d15608",
140
+ "language": "Jupyter",
141
+ "lines": 261,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 7607
145
+ },
146
+ {
147
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/playground_filament3d.ipynb",
148
+ "sha256": "31b92fc79534f0947c4867fdb5b0b634c186a64f53e896a2d02fa3021677343a",
149
+ "language": "Jupyter",
150
+ "lines": 246,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 7554
154
+ },
155
+ {
156
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/playground_gja1.ipynb",
157
+ "sha256": "db676de5336c31dd340d0d831f1902af8fd2d7f82aee9490ca0abb4711c1e928",
158
+ "language": "Jupyter",
159
+ "lines": 230,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 7510
163
+ },
164
+ {
165
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/playground_lamp1.ipynb",
166
+ "sha256": "9f6430fd4b95383579f35de6eabde17e2075f464941a541cecbd59066c867a53",
167
+ "language": "Jupyter",
168
+ "lines": 270,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 7575
172
+ },
173
+ {
174
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/playground_npm1.ipynb",
175
+ "sha256": "00ba8a6c25c5ef80ff308b7873f0b540a5b15c8814b3d160a8723b5f95f370bf",
176
+ "language": "Jupyter",
177
+ "lines": 269,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 7589
181
+ },
182
+ {
183
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/playground_shell.ipynb",
184
+ "sha256": "f41ee418a77e09f4f7b8bb348723ac57693e0a8979d5dc9711cd73ed841d90cb",
185
+ "language": "Jupyter",
186
+ "lines": 199,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 7438
190
+ },
191
+ {
192
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/playground_spotty.ipynb",
193
+ "sha256": "149d3e33b1b077453054a464122113b287866eeb9a08ba53a149277d6613c1c0",
194
+ "language": "Jupyter",
195
+ "lines": 248,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 7505
199
+ },
200
+ {
201
+ "path": "jupyter/notebooks/segmentation/all_structure_playgrounds/playground_st6gal1.ipynb",
202
+ "sha256": "d7b1108e88487680497a9b100ee527501cfcbf8c3c29e3061d72df27bcd2a4e9",
203
+ "language": "Jupyter",
204
+ "lines": 297,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 7620
208
+ },
209
+ {
210
+ "path": "jupyter/notebooks/segmentation/batch-centrosome-segmentation.ipynb",
211
+ "sha256": "0a889a6021b3b70c3af6940156506a6895cde0028a155648661090f6aacba26d",
212
+ "language": "Jupyter",
213
+ "lines": 101,
214
+ "truncated": false,
215
+ "block": 3,
216
+ "row": 7174
217
+ },
218
+ {
219
+ "path": "jupyter/notebooks/segmentation/batch-rna-segmentation.ipynb",
220
+ "sha256": "54ebef03950ae070bced9180199e7715a7d0bd6621fea5f3b2cb5adfcac64a8f",
221
+ "language": "Jupyter",
222
+ "lines": 118,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 7217
226
+ },
227
+ {
228
+ "path": "jupyter/notebooks/segmentation/batch-template-segmentation.ipynb",
229
+ "sha256": "b0f67143ec99b294a7b6c21cd9c17e54458e8c14f1c15511a937b2c330db0a80",
230
+ "language": "Jupyter",
231
+ "lines": 102,
232
+ "truncated": false,
233
+ "block": 3,
234
+ "row": 7151
235
+ },
236
+ {
237
+ "path": "jupyter/notebooks/segmentation/playground_centrosomes.ipynb",
238
+ "sha256": "959bfa0e327762c5979bb1bb9cbcc89f73ca0f097ffe9c2e3e8b43637366c105",
239
+ "language": "Jupyter",
240
+ "lines": 219,
241
+ "truncated": false,
242
+ "block": 3,
243
+ "row": 7507
244
+ },
245
+ {
246
+ "path": "jupyter/notebooks/segmentation/playground_rna.ipynb",
247
+ "sha256": "c239439643d91806509fe1da4339d4f78c19dea0e966b92ce0e7c878279c935c",
248
+ "language": "Jupyter",
249
+ "lines": 257,
250
+ "truncated": false,
251
+ "block": 3,
252
+ "row": 7561
253
+ }
254
+ ]
255
+ }
manifests/ef/github.com__rishigami__swin-transformer-tf.json ADDED
@@ -0,0 +1,48 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/rishigami/swin-transformer-tf",
4
+ "url": "https://github.com/rishigami/Swin-Transformer-TF?utm_source=chatgpt.com",
5
+ "host": "github.com",
6
+ "commit": "bd4d9f1128774dd902369c35ed0434154c233aff",
7
+ "license": "Apache-2.0",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "c71d239df91726fc519c6eb72d318ec65820627232b2f796219e87dcf35d0ab4",
14
+ "language": "License",
15
+ "lines": 201,
16
+ "truncated": false,
17
+ "block": 1,
18
+ "row": 2216
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "dffa1d393f889363fcd78dacae1a7619e4b13e1d6a929bd60159939ea13b67a2",
23
+ "language": "Text",
24
+ "lines": 58,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2465
28
+ },
29
+ {
30
+ "path": "swintransformer/__init__.py",
31
+ "sha256": "f8e12f80062c1ac1c6423c432b72234a63b928342af56ecb29e8176bf1994cb7",
32
+ "language": "Python",
33
+ "lines": 1,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 17390
37
+ },
38
+ {
39
+ "path": "swintransformer/model.py",
40
+ "sha256": "b77385d9c7660e5254fb80eee5b8008c849bbc1f8a6114841c9d3ba09b5d1fa8",
41
+ "language": "Python",
42
+ "lines": 453,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 27042
46
+ }
47
+ ]
48
+ }
manifests/ef/zenodo__20041637.json ADDED
@@ -0,0 +1,39 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:20041637",
4
+ "url": "10.5281/zenodo.20041637",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "CC-BY-4.0",
8
+ "license_confirmed_by": "license of the archive's record",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "Additional_figures.ipynb",
13
+ "sha256": "0cef90fa5c4a09b74ca63c42e4e9c5a909a1d276afad03e588a1ef3d14955aa5",
14
+ "language": "Jupyter",
15
+ "lines": 1149,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 7830
19
+ },
20
+ {
21
+ "path": "External stimuli.ipynb",
22
+ "sha256": "3d7a07d8ace3f38679fefad66917f67dac611cab438425165def5ac1073bf7ff",
23
+ "language": "Jupyter",
24
+ "lines": 167,
25
+ "truncated": false,
26
+ "block": 3,
27
+ "row": 7353
28
+ },
29
+ {
30
+ "path": "Wireless_BSPM.ipynb",
31
+ "sha256": "8715e91d3210f5f964a934acdde9df30faa82ea859f59c06c0eff1acd373c913",
32
+ "language": "Jupyter",
33
+ "lines": 3675,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 7895
37
+ }
38
+ ]
39
+ }
manifests/ef/zenodo__20835637.json ADDED
@@ -0,0 +1,84 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:20835637",
4
+ "url": "https://doi.org/10.5281/zenodo.20835637",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "CC-BY-4.0",
8
+ "license_confirmed_by": "license of the archive's record",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "CIFAR_RGB_digital_backend.m",
13
+ "sha256": "7fc9bb8b8678a097c3aa2fe2eccb5e5f0c657d4017bbc7fb42b03a8339cde86e",
14
+ "language": "MATLAB",
15
+ "lines": 171,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 14609
19
+ },
20
+ {
21
+ "path": "CIFAR_RGB_optical_encryption.m",
22
+ "sha256": "0ea0e9a8fcebef68f77be0912257da11cf990656ce9039d6c70ef46b6fbce0f2",
23
+ "language": "MATLAB",
24
+ "lines": 259,
25
+ "truncated": false,
26
+ "block": 3,
27
+ "row": 15720
28
+ },
29
+ {
30
+ "path": "CIFAR_RGB_optical_neural_network_2SLM.m",
31
+ "sha256": "5c5b2b6524cb4260e3ae39bf9883e86e71f5aee467e49e5a17ceed2aa372c364",
32
+ "language": "MATLAB",
33
+ "lines": 276,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 16059
37
+ },
38
+ {
39
+ "path": "DOP_modulation_calibration_1SLM.m",
40
+ "sha256": "b7b58a5d6b21fefac2b90e79dbdcde694ce11677de4333ae42f7ae217ea17059",
41
+ "language": "MATLAB",
42
+ "lines": 261,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 16054
46
+ },
47
+ {
48
+ "path": "DOP_modulation_calibration_2SLM.m",
49
+ "sha256": "b1c592fe4ef5a7274740ea983ff21d8f99771306998d42e37295c222d8efef76",
50
+ "language": "MATLAB",
51
+ "lines": 236,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 15753
55
+ },
56
+ {
57
+ "path": "README.txt",
58
+ "sha256": "30e59e3b381bad6dcbf798ddbab64da48fd2b7dbb3e39ffbe4c393b82b540c5f",
59
+ "language": "Text",
60
+ "lines": 32,
61
+ "truncated": false,
62
+ "block": 4,
63
+ "row": 2392
64
+ },
65
+ {
66
+ "path": "Spatial_DOP_SOP_modulator_1SLM.m",
67
+ "sha256": "495f267d3ef41aef151e3dcb260a77207aea775922aded7f7131a8b3731b2ca8",
68
+ "language": "MATLAB",
69
+ "lines": 249,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 15534
73
+ },
74
+ {
75
+ "path": "Spatial_DOP_SOP_modulator_2SLM.m",
76
+ "sha256": "9e2bd31132283db7ac5c20a494d5539d4e0d571e89d9487618afd1b0d3cf12db",
77
+ "language": "MATLAB",
78
+ "lines": 249,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 15627
82
+ }
83
+ ]
84
+ }
manifests/f0/github.com__pgmpy__pgmpy.json ADDED
The diff for this file is too large to render. See raw diff
 
manifests/f0/github.com__scikit-fmm__scikit-fmm.json ADDED
@@ -0,0 +1,237 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/scikit-fmm/scikit-fmm",
4
+ "url": "https://github.com/scikit-fmm/scikit-fmm",
5
+ "host": "github.com",
6
+ "commit": "3618765f26fe469163840dd0d9775848ec379c3e",
7
+ "license": "BSD-3-Clause",
8
+ "license_confirmed_by": "license file LICENSE.txt",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE.txt",
13
+ "sha256": "98e292bac9da2ede4d29e0c600fed0705ba642eaa118dfc6d9b202cbb97260e0",
14
+ "language": "License",
15
+ "lines": 31,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8124
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "8a931563e8278c9c922ece7f9bafbc8c9a609f257ff9ab2ce8e81439e66f94cc",
23
+ "language": "Text",
24
+ "lines": 99,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2496
28
+ },
29
+ {
30
+ "path": "doc/conf.py",
31
+ "sha256": "7626ec4cb635c335b1f77b9a3b549f4b3fd78334f2064fd59bf6ab51fc23d06e",
32
+ "language": "Python",
33
+ "lines": 269,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 24823
37
+ },
38
+ {
39
+ "path": "examples/2d_example.py",
40
+ "sha256": "5b9a863dde28423cb78a5792036fbeeb1963e7c756627b610959e9b9d4647eb3",
41
+ "language": "Python",
42
+ "lines": 54,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 19706
46
+ },
47
+ {
48
+ "path": "examples/boundaryconditions_example.py",
49
+ "sha256": "8e02ab8b761542928c3d08c188eac722b396f793d88cb1d5105fb5d9d1fbee7d",
50
+ "language": "Python",
51
+ "lines": 36,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 19093
55
+ },
56
+ {
57
+ "path": "examples/extension_velocities_example.py",
58
+ "sha256": "ee1290b26f4a9540403eade3a613f80b6fb77dc28f7eaabb36021ed04262392d",
59
+ "language": "Python",
60
+ "lines": 31,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 18696
64
+ },
65
+ {
66
+ "path": "profile/prof.cpp",
67
+ "sha256": "7caacde778172070b1b1c4d509b8ae2da21ad05cbe58f48727199dfd5a11a728",
68
+ "language": "C++",
69
+ "lines": 42,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 986
73
+ },
74
+ {
75
+ "path": "profile/prof.sh",
76
+ "sha256": "f0f21087ad10b237fa873b0eb019bafeb972d525057204745f5b62fd07bb756e",
77
+ "language": "Shell",
78
+ "lines": 33,
79
+ "truncated": false,
80
+ "block": 4,
81
+ "row": 1825
82
+ },
83
+ {
84
+ "path": "profile/profile.py",
85
+ "sha256": "f5e0024bd0baee8713c3480fb849751c0416c27f8d344265c7c12361d96ccd54",
86
+ "language": "Python",
87
+ "lines": 31,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 18631
91
+ },
92
+ {
93
+ "path": "skfmm/__init__.py",
94
+ "sha256": "914a5b23157fdfabf5e90b4ffc6968a76a21686d56397e34c2704865032e3f45",
95
+ "language": "Python",
96
+ "lines": 902,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 27694
100
+ },
101
+ {
102
+ "path": "skfmm/base_marcher.cpp",
103
+ "sha256": "b8832403cae5d496fe04c91685b3df5cc2fa1e2dcd299a7e403b452eeea55e24",
104
+ "language": "C++",
105
+ "lines": 225,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 2628
109
+ },
110
+ {
111
+ "path": "skfmm/base_marcher.h",
112
+ "sha256": "b7e9b94efa639150a3f969ecf2413d87b6fcc3aaa5a33f4180764fb3c6950e04",
113
+ "language": "C/C++",
114
+ "lines": 105,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 3927
118
+ },
119
+ {
120
+ "path": "skfmm/distance_marcher.cpp",
121
+ "sha256": "9b8b3281f4ac07e5805d3102518f6de6425cbe983d0bf12a10427dc3a9c9a03e",
122
+ "language": "C++",
123
+ "lines": 166,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 2400
127
+ },
128
+ {
129
+ "path": "skfmm/distance_marcher.h",
130
+ "sha256": "887278de6eae7ecbbc1cf5193b41088ca7e51b834436ff014652ce57e16cad41",
131
+ "language": "C/C++",
132
+ "lines": 23,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 3452
136
+ },
137
+ {
138
+ "path": "skfmm/extension_velocity_marcher.cpp",
139
+ "sha256": "9aa2228de5ac3c0ea372183b5c82efc30de239fa73143cdb01fcbf1523d0d560",
140
+ "language": "C++",
141
+ "lines": 155,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 2381
145
+ },
146
+ {
147
+ "path": "skfmm/extension_velocity_marcher.h",
148
+ "sha256": "ddd0252a1dd1306d5d8bee794ed20705dea267cce47328f19803449b167c3360",
149
+ "language": "C/C++",
150
+ "lines": 27,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 3476
154
+ },
155
+ {
156
+ "path": "skfmm/fmm.cpp",
157
+ "sha256": "421b3d6bd227d12830ff929cacc89da1b2b52e41a90e8991ae3a8e14e9328d51",
158
+ "language": "C++",
159
+ "lines": 337,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 2920
163
+ },
164
+ {
165
+ "path": "skfmm/heap.cpp",
166
+ "sha256": "db749e4d53a77324824e8086ca83517568146a2b6e69e8b78fe616e899d71948",
167
+ "language": "C++",
168
+ "lines": 205,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 2639
172
+ },
173
+ {
174
+ "path": "skfmm/heap.h",
175
+ "sha256": "033314cd39fd3317e28127135820347ae7c8e88fd5ded0811e92e79470e18a9f",
176
+ "language": "C/C++",
177
+ "lines": 60,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 3918
181
+ },
182
+ {
183
+ "path": "skfmm/heap.py",
184
+ "sha256": "688aaef2dbf1ed7aa277a9c19cf53e5905c135e3db3894226d8c719173ee4900",
185
+ "language": "Python",
186
+ "lines": 173,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 22848
190
+ },
191
+ {
192
+ "path": "skfmm/pfmm.py",
193
+ "sha256": "371b0507549e1259be12b1bf582eca054d1c9f61ee61cad59cd76e25fb0c9387",
194
+ "language": "Python",
195
+ "lines": 245,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 25251
199
+ },
200
+ {
201
+ "path": "skfmm/pheap.cpp",
202
+ "sha256": "57585d66382993124d16ac86e4fa54acc8c1b151116db6c1fae3039df499eb51",
203
+ "language": "C++",
204
+ "lines": 5075,
205
+ "truncated": true,
206
+ "block": 3,
207
+ "row": 3305
208
+ },
209
+ {
210
+ "path": "skfmm/travel_time_marcher.cpp",
211
+ "sha256": "c6b2ebf9b15947c79ca12d35df80a5027e9ad677b1fc8cba4e5c6080fdea576d",
212
+ "language": "C++",
213
+ "lines": 118,
214
+ "truncated": false,
215
+ "block": 3,
216
+ "row": 2264
217
+ },
218
+ {
219
+ "path": "skfmm/travel_time_marcher.h",
220
+ "sha256": "5198e302bfa3ddac696361620700d9f4f5bfcc911ca95f4c2c92e1f43a832a86",
221
+ "language": "C/C++",
222
+ "lines": 37,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 3547
226
+ },
227
+ {
228
+ "path": "static_analysis.sh",
229
+ "sha256": "ae2ca4a63682a677aafc0eeedafa24981a51dcbd8869b8b8a629022bd587aaa8",
230
+ "language": "Shell",
231
+ "lines": 20,
232
+ "truncated": false,
233
+ "block": 4,
234
+ "row": 1531
235
+ }
236
+ ]
237
+ }
manifests/f0/zenodo__21076315.json ADDED
@@ -0,0 +1,48 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:21076315",
4
+ "url": "10.5281/zenodo.21076315",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "GPL-3.0",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986",
14
+ "language": "License",
15
+ "lines": 674,
16
+ "truncated": false,
17
+ "block": 1,
18
+ "row": 2235
19
+ },
20
+ {
21
+ "path": "R Scripts/AnalysisPipeline.R",
22
+ "sha256": "d291bd9e6035381e8b23467eda55fa73f900fee15991da4bef4481637d53115c",
23
+ "language": "R",
24
+ "lines": 201,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 983
28
+ },
29
+ {
30
+ "path": "R Scripts/readLuminexExcelFile_ver1_03.R",
31
+ "sha256": "ca4305efb76d74871eb8d7f0b6c835feaabafd0011ec705040a5ced2ce975e57",
32
+ "language": "R",
33
+ "lines": 842,
34
+ "truncated": false,
35
+ "block": 4,
36
+ "row": 1178
37
+ },
38
+ {
39
+ "path": "README.md",
40
+ "sha256": "9d4d2ac0872badaff3104b6db745066dde6c944e1d51f5d7f02e7fa6c9a55141",
41
+ "language": "Text",
42
+ "lines": 38,
43
+ "truncated": false,
44
+ "block": 4,
45
+ "row": 2344
46
+ }
47
+ ]
48
+ }
manifests/f1/github.com__hakyimlab__metaxcan.json ADDED
@@ -0,0 +1,1047 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/hakyimlab/metaxcan",
4
+ "url": "https://github.com/hakyimlab/MetaXcan",
5
+ "host": "github.com",
6
+ "commit": "e069063a10539fe92adadb645fc667a40c2cf885",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "DevNotes.Rmd",
13
+ "sha256": "669a63fe395151b966c147ddcf1175e71a16b536073bf19384c2a9da9879690a",
14
+ "language": "R",
15
+ "lines": 13,
16
+ "truncated": false,
17
+ "block": 4,
18
+ "row": 192
19
+ },
20
+ {
21
+ "path": "LICENSE",
22
+ "sha256": "8df49762788cf61cb392f8188d9c8247081fc6147e38a79e0924887807f18d52",
23
+ "language": "License",
24
+ "lines": 23,
25
+ "truncated": false,
26
+ "block": 3,
27
+ "row": 8087
28
+ },
29
+ {
30
+ "path": "README.md",
31
+ "sha256": "f04d022fb535a95e2256b1b1aa25ab11806734f76c7ecf9717e6a2bc38135da0",
32
+ "language": "Text",
33
+ "lines": 313,
34
+ "truncated": false,
35
+ "block": 4,
36
+ "row": 2721
37
+ },
38
+ {
39
+ "path": "software/BuildExpressionProduct.py",
40
+ "sha256": "f07d715cf1d3138e7304cc3d86db7108f264cfb13da2d96026d524b45b2da53c",
41
+ "language": "Python",
42
+ "lines": 63,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 20853
46
+ },
47
+ {
48
+ "path": "software/CovarianceBuilder.py",
49
+ "sha256": "7a5103f5b1aecd2380324eeef3cf140d75c02755ec8a460255cf593127f958be",
50
+ "language": "Python",
51
+ "lines": 88,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 22373
55
+ },
56
+ {
57
+ "path": "software/M00_prerequisites.py",
58
+ "sha256": "580d0708964eeaf293fe6760e50ae7cabe06dcf49f4e6f8a2b6a46f01bc98514",
59
+ "language": "Python",
60
+ "lines": 176,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 24551
64
+ },
65
+ {
66
+ "path": "software/M01_covariances_correlations.py",
67
+ "sha256": "cb5e81bc4eac139aa0a03c7af7d4b9843568a4cf194e9de0c0010789073e60ed",
68
+ "language": "Python",
69
+ "lines": 358,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 26305
73
+ },
74
+ {
75
+ "path": "software/M02_variances.py",
76
+ "sha256": "5e99889d68a69ba03a7aab8f7d68b52ca55b46b3481bf291f977cddf9bf5c08e",
77
+ "language": "Python",
78
+ "lines": 83,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 21277
82
+ },
83
+ {
84
+ "path": "software/M03_betas.py",
85
+ "sha256": "c32709a578e8a33a22491293056242521acc4d01bce9cbcd4c8d192a57ed485d",
86
+ "language": "Python",
87
+ "lines": 188,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 24627
91
+ },
92
+ {
93
+ "path": "software/M04_zscores.py",
94
+ "sha256": "b4acb5be5a0ba27043d3d9353d8c21fd059338118c12c40d6bb487c8d923d2a3",
95
+ "language": "Python",
96
+ "lines": 152,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 23764
100
+ },
101
+ {
102
+ "path": "software/MPSimulation.py",
103
+ "sha256": "fa389e00bb21607b856223514858d7bed265969753925dec0debeaed899b94c7",
104
+ "language": "Python",
105
+ "lines": 101,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 22711
109
+ },
110
+ {
111
+ "path": "software/MetaMany.py",
112
+ "sha256": "194af18ff34ac30a4481a02f912eb686c542d59dacd279f62b322d5430e84e64",
113
+ "language": "Python",
114
+ "lines": 163,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 24509
118
+ },
119
+ {
120
+ "path": "software/MetaXcanUI.py",
121
+ "sha256": "5212dc551938e906e7ac5b5942744f1e6846d9086de1c3f67d4a9940b78a4363",
122
+ "language": "Python",
123
+ "lines": 44,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 19417
127
+ },
128
+ {
129
+ "path": "software/MulTiXcan.py",
130
+ "sha256": "ef0c8dff1523a924d5cf92e97351a4638097e8dc18bb4db77d552f6dc4e4d529",
131
+ "language": "Python",
132
+ "lines": 110,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 23461
136
+ },
137
+ {
138
+ "path": "software/PrediXcan.py",
139
+ "sha256": "8d3d5a1d0eca25edaaeb439a2ef6323d5dceda064e046d82676368114bdb6d38",
140
+ "language": "Python",
141
+ "lines": 45,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 19372
145
+ },
146
+ {
147
+ "path": "software/PrediXcanAssociation.py",
148
+ "sha256": "0f2660c4f8ff219e48290eac78b06c277d8798aa35019715b86670b9cebe5d83",
149
+ "language": "Python",
150
+ "lines": 83,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 21981
154
+ },
155
+ {
156
+ "path": "software/Predict.py",
157
+ "sha256": "7dae9ddf2eaa711673d0a1e55fb718ab7e082471cb21c5b4a8271e3659697c61",
158
+ "language": "Python",
159
+ "lines": 281,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 26188
163
+ },
164
+ {
165
+ "path": "software/SMulTiXcan.py",
166
+ "sha256": "6c6cc559f6d91bab7e60e29a46051cc2e40c6d4a3e3768db685fd355be2a7397",
167
+ "language": "Python",
168
+ "lines": 100,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 23224
172
+ },
173
+ {
174
+ "path": "software/SPrediXcan.py",
175
+ "sha256": "94e79ae2eb42b8875f1696e8d7b371385f680f8d1dbb3fb44b8818f250fd2fcd",
176
+ "language": "Python",
177
+ "lines": 77,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 21917
181
+ },
182
+ {
183
+ "path": "software/ToHDF5.py",
184
+ "sha256": "706ab5c5645c9a653e025a3c216a32e32cc22ca4a1dc3a03b49a8e84638d652a",
185
+ "language": "Python",
186
+ "lines": 61,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 20119
190
+ },
191
+ {
192
+ "path": "software/build_minimal_data_requirements.sh",
193
+ "sha256": "84723c9301d8775e2af0d2bc2e9e24433ebdfb2a84e91fb8df7425e2b61be839",
194
+ "language": "Shell",
195
+ "lines": 23,
196
+ "truncated": false,
197
+ "block": 4,
198
+ "row": 1613
199
+ },
200
+ {
201
+ "path": "software/build_minimal_example_data.sh",
202
+ "sha256": "825d46e5222dcbd5c94636e506f021d87a5e7a3158a68e8590d57ca9bd57ff6a",
203
+ "language": "Shell",
204
+ "lines": 11,
205
+ "truncated": false,
206
+ "block": 4,
207
+ "row": 1376
208
+ },
209
+ {
210
+ "path": "software/ez_setup.py",
211
+ "sha256": "21adece197914a37445a4eecaf9c7e278ff6429716c5d6340cd225ce057e62b9",
212
+ "language": "Python",
213
+ "lines": 391,
214
+ "truncated": false,
215
+ "block": 3,
216
+ "row": 25741
217
+ },
218
+ {
219
+ "path": "software/metax/Constants.py",
220
+ "sha256": "b3f516142067c64646faec5d6d35fcc6524be05275cc25a16f4696100bf46396",
221
+ "language": "Python",
222
+ "lines": 16,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 17836
226
+ },
227
+ {
228
+ "path": "software/metax/DataSet.py",
229
+ "sha256": "ee1ee31c5842b8363fbaee0f26fbd4ff5ff85ecb385823b037fbe8d17c80108c",
230
+ "language": "Python",
231
+ "lines": 50,
232
+ "truncated": false,
233
+ "block": 3,
234
+ "row": 19533
235
+ },
236
+ {
237
+ "path": "software/metax/DataSetSNP.py",
238
+ "sha256": "389bfed7e33aa96724a33aa834828cedc3addf9be7e1033d706ab6b509b1eedf",
239
+ "language": "Python",
240
+ "lines": 11,
241
+ "truncated": false,
242
+ "block": 3,
243
+ "row": 18196
244
+ },
245
+ {
246
+ "path": "software/metax/Exceptions.py",
247
+ "sha256": "76328bfc6cdf147feb946e9926b6d0958bdb9b2d5837109722249466ef903dd6",
248
+ "language": "Python",
249
+ "lines": 49,
250
+ "truncated": false,
251
+ "block": 3,
252
+ "row": 20009
253
+ },
254
+ {
255
+ "path": "software/metax/Formats.py",
256
+ "sha256": "0a11a93da4349767f680e08f33c2c07e73ac0ca8f94a3151556f70d324312152",
257
+ "language": "Python",
258
+ "lines": 7,
259
+ "truncated": false,
260
+ "block": 3,
261
+ "row": 17578
262
+ },
263
+ {
264
+ "path": "software/metax/Gene.py",
265
+ "sha256": "1b6fdb5eb63f4beac3408db211fd8aa436ae8793a2aa99b9f23b10257098615f",
266
+ "language": "Python",
267
+ "lines": 56,
268
+ "truncated": false,
269
+ "block": 3,
270
+ "row": 20111
271
+ },
272
+ {
273
+ "path": "software/metax/KeyedDataSet.py",
274
+ "sha256": "bb265f00e613c198795459e6808b0f9b805327428399b0b21cad98c932f2ef69",
275
+ "language": "Python",
276
+ "lines": 156,
277
+ "truncated": false,
278
+ "block": 3,
279
+ "row": 23351
280
+ },
281
+ {
282
+ "path": "software/metax/Logging.py",
283
+ "sha256": "d134ae8174abeb58ebf6f2bbb8a69d1ea6982c9727ee44bb745e71b87421fa04",
284
+ "language": "Python",
285
+ "lines": 34,
286
+ "truncated": false,
287
+ "block": 3,
288
+ "row": 18938
289
+ },
290
+ {
291
+ "path": "software/metax/MainScreen.py",
292
+ "sha256": "e5471d3fb21745212d90b135e4a3067bc8ed6384107feea2fa2edb912d12b8d6",
293
+ "language": "Python",
294
+ "lines": 379,
295
+ "truncated": false,
296
+ "block": 3,
297
+ "row": 26054
298
+ },
299
+ {
300
+ "path": "software/metax/MainScreenView.py",
301
+ "sha256": "10bd5c9b4a0d829b3494dde403008978fc4ba2c0c400faa7c541c41a1870b972",
302
+ "language": "Python",
303
+ "lines": 282,
304
+ "truncated": false,
305
+ "block": 3,
306
+ "row": 25783
307
+ },
308
+ {
309
+ "path": "software/metax/MatrixManager.py",
310
+ "sha256": "259cafb6404921db4c46cb679435d7095629770a97bb334eddb092ee788c9755",
311
+ "language": "Python",
312
+ "lines": 237,
313
+ "truncated": false,
314
+ "block": 3,
315
+ "row": 24403
316
+ },
317
+ {
318
+ "path": "software/metax/MatrixManager2.py",
319
+ "sha256": "6f046f94bac2434bf8adddaffe5f07ae096af5867f09f453c0f2850f2099e945",
320
+ "language": "Python",
321
+ "lines": 87,
322
+ "truncated": false,
323
+ "block": 3,
324
+ "row": 20932
325
+ },
326
+ {
327
+ "path": "software/metax/MetaXcanUITask.py",
328
+ "sha256": "2264a66222dab6cf14b677b478a6ae9867460ed97f1234cad39dfc235ae6b5e6",
329
+ "language": "Python",
330
+ "lines": 61,
331
+ "truncated": false,
332
+ "block": 3,
333
+ "row": 19584
334
+ },
335
+ {
336
+ "path": "software/metax/NamingConventions.py",
337
+ "sha256": "c2b04e420bb79647d4461b8753466276fd0553353c216ea360d0702975614711",
338
+ "language": "Python",
339
+ "lines": 130,
340
+ "truncated": false,
341
+ "block": 3,
342
+ "row": 23028
343
+ },
344
+ {
345
+ "path": "software/metax/Person.py",
346
+ "sha256": "4ecf8b24e0e4f50774a6060875ec0804724eb2994e9a2ffe7300468f29701d18",
347
+ "language": "Python",
348
+ "lines": 86,
349
+ "truncated": false,
350
+ "block": 3,
351
+ "row": 21152
352
+ },
353
+ {
354
+ "path": "software/metax/PrediXcanFormatUtilities.py",
355
+ "sha256": "ebf8da70e71a365090e3472e0eaf01a59dffd8f1f581d1fa2c80d878c5a0f7ec",
356
+ "language": "Python",
357
+ "lines": 189,
358
+ "truncated": false,
359
+ "block": 3,
360
+ "row": 24615
361
+ },
362
+ {
363
+ "path": "software/metax/PredictionModel.py",
364
+ "sha256": "586da7735d5b706788429024a2d3028e378b0946a41ff171a70fdbcf7e861595",
365
+ "language": "Python",
366
+ "lines": 315,
367
+ "truncated": false,
368
+ "block": 3,
369
+ "row": 25468
370
+ },
371
+ {
372
+ "path": "software/metax/ThousandGenomesUtilities.py",
373
+ "sha256": "54cf610c5090d189872e4aae9d9d33da0b10d17bb640712c16524cab5acf7b90",
374
+ "language": "Python",
375
+ "lines": 281,
376
+ "truncated": false,
377
+ "block": 3,
378
+ "row": 25905
379
+ },
380
+ {
381
+ "path": "software/metax/Utilities.py",
382
+ "sha256": "489d85b54b9de59688cd36cc4a131f51292a951944f93a4202d37519224b5110",
383
+ "language": "Python",
384
+ "lines": 254,
385
+ "truncated": false,
386
+ "block": 3,
387
+ "row": 24629
388
+ },
389
+ {
390
+ "path": "software/metax/WeightDBUtilities.py",
391
+ "sha256": "7aa0e51d27aa84459399d16e18677a85e4a2b6a4057624d4e3dfa954f89c1877",
392
+ "language": "Python",
393
+ "lines": 170,
394
+ "truncated": false,
395
+ "block": 3,
396
+ "row": 23622
397
+ },
398
+ {
399
+ "path": "software/metax/__init__.py",
400
+ "sha256": "e77c21002293facc428185dd8d7f4ac5f116a452bc4086625a4ff35d8f01f181",
401
+ "language": "Python",
402
+ "lines": 5,
403
+ "truncated": false,
404
+ "block": 3,
405
+ "row": 17537
406
+ },
407
+ {
408
+ "path": "software/metax/cross_model/JointAnalysis.py",
409
+ "sha256": "e5ecfb46f0c7bcfec4792a810320bbed6fd7d3dafe3b01b612c5cdfbc61bc829",
410
+ "language": "Python",
411
+ "lines": 150,
412
+ "truncated": false,
413
+ "block": 3,
414
+ "row": 23890
415
+ },
416
+ {
417
+ "path": "software/metax/cross_model/Utilities.py",
418
+ "sha256": "4a5e9f092e7f08daadd12b8bc954f0d6a6fb8fbf3ab16f9b86e24d1cdd964696",
419
+ "language": "Python",
420
+ "lines": 211,
421
+ "truncated": false,
422
+ "block": 3,
423
+ "row": 24753
424
+ },
425
+ {
426
+ "path": "software/metax/deprecated/DBLoaders.py",
427
+ "sha256": "50b5c8366a86b91a08eff9e0bae452d11e4b9a5993b9aa7eff29e3fc6bf08645",
428
+ "language": "Python",
429
+ "lines": 93,
430
+ "truncated": false,
431
+ "block": 3,
432
+ "row": 21072
433
+ },
434
+ {
435
+ "path": "software/metax/deprecated/MatrixUtilities.py",
436
+ "sha256": "ac6b82704dc8d3f4e8f0803d87b2b9d96c4e4eadf7f1805bc08dce66b66adf2c",
437
+ "language": "Python",
438
+ "lines": 92,
439
+ "truncated": false,
440
+ "block": 3,
441
+ "row": 21079
442
+ },
443
+ {
444
+ "path": "software/metax/deprecated/MethodGuessing.py",
445
+ "sha256": "92472fbe2ec4ccd39146583fe3a1d126833636d75e26794e06c42069682d8c18",
446
+ "language": "Python",
447
+ "lines": 72,
448
+ "truncated": false,
449
+ "block": 3,
450
+ "row": 21467
451
+ },
452
+ {
453
+ "path": "software/metax/deprecated/Normalization.py",
454
+ "sha256": "60e19795e8ce46e7576fbc6d91a6f7dcbba4419f9f66797b7150f3b9f1f1a30e",
455
+ "language": "Python",
456
+ "lines": 126,
457
+ "truncated": false,
458
+ "block": 3,
459
+ "row": 21960
460
+ },
461
+ {
462
+ "path": "software/metax/deprecated/SQLUtilities.py",
463
+ "sha256": "85199e6bb7741e9dfcf54b136ec9bb37de82c8a8e21eff6c8a8c68d0b66513f7",
464
+ "language": "Python",
465
+ "lines": 211,
466
+ "truncated": false,
467
+ "block": 3,
468
+ "row": 23932
469
+ },
470
+ {
471
+ "path": "software/metax/deprecated/ZScoreCalculation.py",
472
+ "sha256": "253a0d5d33537cd0990295ef061a003bc3f668c97b39a0412fc019bc5ea99f27",
473
+ "language": "Python",
474
+ "lines": 210,
475
+ "truncated": false,
476
+ "block": 3,
477
+ "row": 24306
478
+ },
479
+ {
480
+ "path": "software/metax/expression/Expression.py",
481
+ "sha256": "bbbcb5ad4f9b64d5c1ae959d3c5de4a4e2189cb6de3e15c0bbce17c76e161278",
482
+ "language": "Python",
483
+ "lines": 30,
484
+ "truncated": false,
485
+ "block": 3,
486
+ "row": 18872
487
+ },
488
+ {
489
+ "path": "software/metax/expression/HDF5Expression.py",
490
+ "sha256": "66144a191ff17112faad9df6dcfe40912cb97bf1115bb7072b9e990721ca88e0",
491
+ "language": "Python",
492
+ "lines": 164,
493
+ "truncated": false,
494
+ "block": 3,
495
+ "row": 22478
496
+ },
497
+ {
498
+ "path": "software/metax/expression/PlainTextExpression.py",
499
+ "sha256": "4c22674d06d6db29a0e18ba297e1bf1ab01d3e18a557f77c20783cbd0f565961",
500
+ "language": "Python",
501
+ "lines": 130,
502
+ "truncated": false,
503
+ "block": 3,
504
+ "row": 22024
505
+ },
506
+ {
507
+ "path": "software/metax/genotype/BGENGenotype.py",
508
+ "sha256": "9748f8ab029f7407427b9223a6360e82b0b211209c9f3cda6d96ba54d705dec0",
509
+ "language": "Python",
510
+ "lines": 73,
511
+ "truncated": false,
512
+ "block": 3,
513
+ "row": 21132
514
+ },
515
+ {
516
+ "path": "software/metax/genotype/CYVCF2Genotype.py",
517
+ "sha256": "38d3344a69baadd6d2ceba9e163e9ce11580b7376b3540c211e158cb3951bba7",
518
+ "language": "Python",
519
+ "lines": 83,
520
+ "truncated": false,
521
+ "block": 3,
522
+ "row": 21357
523
+ },
524
+ {
525
+ "path": "software/metax/genotype/DosageGenotype.py",
526
+ "sha256": "f6eea02da3d52b44fc99f6978e19a840217f29696052348e3e6da06c439b2d77",
527
+ "language": "Python",
528
+ "lines": 104,
529
+ "truncated": false,
530
+ "block": 3,
531
+ "row": 22259
532
+ },
533
+ {
534
+ "path": "software/metax/genotype/GTExGenotype.py",
535
+ "sha256": "75d49273b3b984d9cd4cc3ab0f9ce29bab30ae8a3ae891bfade2f62fc33142bf",
536
+ "language": "Python",
537
+ "lines": 96,
538
+ "truncated": false,
539
+ "block": 3,
540
+ "row": 21666
541
+ },
542
+ {
543
+ "path": "software/metax/genotype/GeneExpressionMatrixManager.py",
544
+ "sha256": "4a8418d330f016cd61a70710ac65b70cb2282d086c46a0bb85c2250401d6b5ab",
545
+ "language": "Python",
546
+ "lines": 158,
547
+ "truncated": false,
548
+ "block": 3,
549
+ "row": 23435
550
+ },
551
+ {
552
+ "path": "software/metax/genotype/Genotype.py",
553
+ "sha256": "f072e55cd11100fa4f789e984c330716cd7428c25df0ed59409413fa241f38b3",
554
+ "language": "Python",
555
+ "lines": 33,
556
+ "truncated": false,
557
+ "block": 3,
558
+ "row": 18934
559
+ },
560
+ {
561
+ "path": "software/metax/genotype/GenotypeAnalysis.py",
562
+ "sha256": "01f8d4a9cf5dd23a7d65d3e9c06f83861731354f673f4257051bee70f7730b8a",
563
+ "language": "Python",
564
+ "lines": 99,
565
+ "truncated": false,
566
+ "block": 3,
567
+ "row": 21505
568
+ },
569
+ {
570
+ "path": "software/metax/genotype/Helpers.py",
571
+ "sha256": "ba256828fb127f1b2d073ad9678e7c0778998acaef2b16c0fc7125888c9a09b3",
572
+ "language": "Python",
573
+ "lines": 17,
574
+ "truncated": false,
575
+ "block": 3,
576
+ "row": 18861
577
+ },
578
+ {
579
+ "path": "software/metax/genotype/ModelTrainingGenotype.py",
580
+ "sha256": "2d6c3bd59ec560eafffd03be3017731bef81f878002c3ef0b4dbeb7bf9a95448",
581
+ "language": "Python",
582
+ "lines": 75,
583
+ "truncated": false,
584
+ "block": 3,
585
+ "row": 20820
586
+ },
587
+ {
588
+ "path": "software/metax/genotype/PYVCFGenotype.py",
589
+ "sha256": "8294f68b3a95f6d77bf0a4060aba1d5cb05e9f10967be9f5d66555f0211857ad",
590
+ "language": "Python",
591
+ "lines": 69,
592
+ "truncated": false,
593
+ "block": 3,
594
+ "row": 20318
595
+ },
596
+ {
597
+ "path": "software/metax/genotype/Utilities.py",
598
+ "sha256": "7a761246d870aa9fcd3c705693d5b03a84619e6b35ada2c98105f01040a8ffd0",
599
+ "language": "Python",
600
+ "lines": 15,
601
+ "truncated": false,
602
+ "block": 3,
603
+ "row": 18789
604
+ },
605
+ {
606
+ "path": "software/metax/gwas/GWAS.py",
607
+ "sha256": "3d07d9de1dea393d2ae20d6cbaed7e39c313a9a5cd8afe4930a96e2937ffac76",
608
+ "language": "Python",
609
+ "lines": 290,
610
+ "truncated": false,
611
+ "block": 3,
612
+ "row": 25545
613
+ },
614
+ {
615
+ "path": "software/metax/gwas/GWASSpecialHandling.py",
616
+ "sha256": "98efc9e9e4ce49a7c09833d1befec4d422852183b67b1419c34c9bba478a79ed",
617
+ "language": "Python",
618
+ "lines": 90,
619
+ "truncated": false,
620
+ "block": 3,
621
+ "row": 21501
622
+ },
623
+ {
624
+ "path": "software/metax/gwas/Utilities.py",
625
+ "sha256": "63983782d22e38217c610c1e6c47d0a1db7f5ba752cdb8dd46d95a4a0bdfb179",
626
+ "language": "Python",
627
+ "lines": 122,
628
+ "truncated": false,
629
+ "block": 3,
630
+ "row": 24017
631
+ },
632
+ {
633
+ "path": "software/metax/metaxcan/AssociationCalculation.py",
634
+ "sha256": "b1cd8ec0455f5d165e5a5914dfc8353709558799940f1c2afc12e8c99cbdcf6d",
635
+ "language": "Python",
636
+ "lines": 132,
637
+ "truncated": false,
638
+ "block": 3,
639
+ "row": 22248
640
+ },
641
+ {
642
+ "path": "software/metax/metaxcan/MetaXcanResultsManager.py",
643
+ "sha256": "1d11fd56e10ad9c01ae54f4bd34fbe91a8b380bd6d6684ccd88efec2f6fca832",
644
+ "language": "Python",
645
+ "lines": 84,
646
+ "truncated": false,
647
+ "block": 3,
648
+ "row": 20631
649
+ },
650
+ {
651
+ "path": "software/metax/metaxcan/Utilities.py",
652
+ "sha256": "ceca0876e7c612f6b20c6df39949c71efcbb70a8641cfc384f49a4e1931e1665",
653
+ "language": "Python",
654
+ "lines": 347,
655
+ "truncated": false,
656
+ "block": 3,
657
+ "row": 25887
658
+ },
659
+ {
660
+ "path": "software/metax/misc/DataFrameStreamer.py",
661
+ "sha256": "03cfc56af928a386489b75ce3a229c0598e9a85abac44ba87346afd7deb5043e",
662
+ "language": "Python",
663
+ "lines": 83,
664
+ "truncated": false,
665
+ "block": 3,
666
+ "row": 21088
667
+ },
668
+ {
669
+ "path": "software/metax/misc/FeatureMatrix.py",
670
+ "sha256": "e413cbff10f68ad54ddc5c1c56d7f8615b462fa19d159b5406aacd672d982d1a",
671
+ "language": "Python",
672
+ "lines": 128,
673
+ "truncated": false,
674
+ "block": 3,
675
+ "row": 22527
676
+ },
677
+ {
678
+ "path": "software/metax/misc/GWASAndModels.py",
679
+ "sha256": "459e30aacca54bcff09e458bd74a858428883c2982adde662dcd6ca688beb2ed",
680
+ "language": "Python",
681
+ "lines": 82,
682
+ "truncated": false,
683
+ "block": 3,
684
+ "row": 21355
685
+ },
686
+ {
687
+ "path": "software/metax/misc/Genomics.py",
688
+ "sha256": "816f87914bfbab3a3fc5acc95486296fdc6dc56a340fdc08e91b02978fd4ffc4",
689
+ "language": "Python",
690
+ "lines": 118,
691
+ "truncated": false,
692
+ "block": 3,
693
+ "row": 21625
694
+ },
695
+ {
696
+ "path": "software/metax/misc/KeyedDataSource.py",
697
+ "sha256": "4c0512813547b69069bd4f56ce783683a571a564bb32db27a0e0b22ac0abd667",
698
+ "language": "Python",
699
+ "lines": 82,
700
+ "truncated": false,
701
+ "block": 3,
702
+ "row": 20511
703
+ },
704
+ {
705
+ "path": "software/metax/misc/Math.py",
706
+ "sha256": "e66e2503c47b523ce907e789672ce4d0da9750227f9fab61cfbc222b9c9df483",
707
+ "language": "Python",
708
+ "lines": 69,
709
+ "truncated": false,
710
+ "block": 3,
711
+ "row": 20092
712
+ },
713
+ {
714
+ "path": "software/metax/predixcan/MultiPrediXcanAssociation.py",
715
+ "sha256": "590898cb247223a92acdbdd0e48fb4a7cccc3afed1e64e23b57f15d7678cd94e",
716
+ "language": "Python",
717
+ "lines": 240,
718
+ "truncated": false,
719
+ "block": 3,
720
+ "row": 24873
721
+ },
722
+ {
723
+ "path": "software/metax/predixcan/PrediXcanAssociation.py",
724
+ "sha256": "93aea995c71599c461f9e607e79980d87df0eecb9014346ed161701640fb80f0",
725
+ "language": "Python",
726
+ "lines": 136,
727
+ "truncated": false,
728
+ "block": 3,
729
+ "row": 22266
730
+ },
731
+ {
732
+ "path": "software/metax/predixcan/Simulations.py",
733
+ "sha256": "5c0873d05f7b2aa95ea319a41162ad92b41478c0c6d4aaee08b9423984118931",
734
+ "language": "Python",
735
+ "lines": 253,
736
+ "truncated": false,
737
+ "block": 3,
738
+ "row": 25246
739
+ },
740
+ {
741
+ "path": "software/metax/predixcan/Utilities.py",
742
+ "sha256": "117e369f4fa7ec0214b3404d0e8067978fb56de06815ae5c4d0dccbda434ae04",
743
+ "language": "Python",
744
+ "lines": 360,
745
+ "truncated": false,
746
+ "block": 3,
747
+ "row": 26110
748
+ },
749
+ {
750
+ "path": "software/setup.py",
751
+ "sha256": "76603d15f5526332c41f25fd5317f9adbb15afb365a30ea83e9b60eceaedcac6",
752
+ "language": "Python",
753
+ "lines": 56,
754
+ "truncated": false,
755
+ "block": 3,
756
+ "row": 20433
757
+ },
758
+ {
759
+ "path": "software/tests/CreateGTExLike.py",
760
+ "sha256": "5a4ba8245a6dc3769a2e31fa20ba5910233ad0b389478319608cbbf0491117be",
761
+ "language": "Python",
762
+ "lines": 147,
763
+ "truncated": false,
764
+ "block": 3,
765
+ "row": 22947
766
+ },
767
+ {
768
+ "path": "software/tests/SampleData.py",
769
+ "sha256": "a07b74047ae2eb3f68f100ad5639344333595242942821ac6af9b31c2a3d3dfa",
770
+ "language": "Python",
771
+ "lines": 295,
772
+ "truncated": false,
773
+ "block": 3,
774
+ "row": 25498
775
+ },
776
+ {
777
+ "path": "software/tests/__init__.py",
778
+ "sha256": "5f2b71da8f6362425593634a63316bfd94074caf988097e0f60fbb983c20591c",
779
+ "language": "Python",
780
+ "lines": 6,
781
+ "truncated": false,
782
+ "block": 3,
783
+ "row": 17499
784
+ },
785
+ {
786
+ "path": "software/tests/_td/beta_builder.R",
787
+ "sha256": "935bfed5d5e0709223d65a1d7de254f426afb50adfd0b7ee7dae60d5d24d0c5a",
788
+ "language": "R",
789
+ "lines": 6,
790
+ "truncated": false,
791
+ "block": 4,
792
+ "row": 157
793
+ },
794
+ {
795
+ "path": "software/tests/_td/convert_model_to_text.py",
796
+ "sha256": "f9e833bbe762aa34e77872ee3165593d34a13ed25875e131478c96f8ea83cd33",
797
+ "language": "Python",
798
+ "lines": 39,
799
+ "truncated": false,
800
+ "block": 3,
801
+ "row": 19229
802
+ },
803
+ {
804
+ "path": "software/tests/_td/trim_data_for_multi_tissue_test.py",
805
+ "sha256": "2a53058244e2831b62b1469cbab80d30133520e32fb7eaf2f7ed169bb3515321",
806
+ "language": "Python",
807
+ "lines": 46,
808
+ "truncated": false,
809
+ "block": 3,
810
+ "row": 19638
811
+ },
812
+ {
813
+ "path": "software/tests/cov_data.py",
814
+ "sha256": "f4588033b93d80993d77bac4ca27a650c50f2558c92ab092cce2c8e74a063e0f",
815
+ "language": "Python",
816
+ "lines": 45,
817
+ "truncated": false,
818
+ "block": 3,
819
+ "row": 20234
820
+ },
821
+ {
822
+ "path": "software/tests/gen_data.py",
823
+ "sha256": "62be8ea4a8db131ade52f2c8967cba15802f7026f390372dd82c840f4a94fba6",
824
+ "language": "Python",
825
+ "lines": 15,
826
+ "truncated": false,
827
+ "block": 3,
828
+ "row": 18319
829
+ },
830
+ {
831
+ "path": "software/tests/scz2_sample.py",
832
+ "sha256": "8e08dec095a64f513b9ae0047dfa77acc4e06f163b285c2b976f866792da6a45",
833
+ "language": "Python",
834
+ "lines": 17,
835
+ "truncated": false,
836
+ "block": 3,
837
+ "row": 19887
838
+ },
839
+ {
840
+ "path": "software/tests/test_M00_prerequisites.py",
841
+ "sha256": "baf84042fd7be982b351bd523f0a44af21529ccc12673694cf5e19a3fcca1159",
842
+ "language": "Python",
843
+ "lines": 103,
844
+ "truncated": false,
845
+ "block": 3,
846
+ "row": 22062
847
+ },
848
+ {
849
+ "path": "software/tests/test_M01_covariances_correlations.py",
850
+ "sha256": "335c980f784297aea7f0478f5309664ed62a4913746ca49c857acbfe60a0e12f",
851
+ "language": "Python",
852
+ "lines": 95,
853
+ "truncated": false,
854
+ "block": 3,
855
+ "row": 21590
856
+ },
857
+ {
858
+ "path": "software/tests/test_M03_betas.py",
859
+ "sha256": "b1866622d91683401bf16ab452eed43d8119d51f91649348e24cecd17de67b2a",
860
+ "language": "Python",
861
+ "lines": 249,
862
+ "truncated": false,
863
+ "block": 3,
864
+ "row": 24578
865
+ },
866
+ {
867
+ "path": "software/tests/test_Person.py",
868
+ "sha256": "2a21519eaa796c24e097874a06740ede5a6991fe490ad0e9e36a56e062a5c961",
869
+ "language": "Python",
870
+ "lines": 198,
871
+ "truncated": false,
872
+ "block": 3,
873
+ "row": 24906
874
+ },
875
+ {
876
+ "path": "software/tests/test_association_calculation.py",
877
+ "sha256": "cf44b0e745f2b7e110191375d1d1c2129bca973b77e9a00eb7dd0c8d284bc69d",
878
+ "language": "Python",
879
+ "lines": 97,
880
+ "truncated": false,
881
+ "block": 3,
882
+ "row": 22461
883
+ },
884
+ {
885
+ "path": "software/tests/test_dataframe_streamer.py",
886
+ "sha256": "d772e7f0b3ced204f318b5628327613c8db09ae5365f5192022463048c66d461",
887
+ "language": "Python",
888
+ "lines": 30,
889
+ "truncated": false,
890
+ "block": 3,
891
+ "row": 18682
892
+ },
893
+ {
894
+ "path": "software/tests/test_dataset.py",
895
+ "sha256": "88579fb7a638b639d7b2b617eaf1a7c477bcacd0dc13dcec34cde57874e6dfac",
896
+ "language": "Python",
897
+ "lines": 71,
898
+ "truncated": false,
899
+ "block": 3,
900
+ "row": 20496
901
+ },
902
+ {
903
+ "path": "software/tests/test_dataset_snp.py",
904
+ "sha256": "3766d0dd55d8da505249eb037873b663284f8531343f0aabf616bde927b6bfc4",
905
+ "language": "Python",
906
+ "lines": 47,
907
+ "truncated": false,
908
+ "block": 3,
909
+ "row": 19580
910
+ },
911
+ {
912
+ "path": "software/tests/test_dbloaders.py",
913
+ "sha256": "b2faf4424ac265debc5ee8d7a4429b7a73afd20b2581e18358ef42868e240438",
914
+ "language": "Python",
915
+ "lines": 152,
916
+ "truncated": false,
917
+ "block": 3,
918
+ "row": 23609
919
+ },
920
+ {
921
+ "path": "software/tests/test_feature_matrix.py",
922
+ "sha256": "8ebafebf02b7288d5b825028ac23da6ce48e4a32b691e6b93c2b70dd77986cdb",
923
+ "language": "Python",
924
+ "lines": 66,
925
+ "truncated": false,
926
+ "block": 3,
927
+ "row": 20424
928
+ },
929
+ {
930
+ "path": "software/tests/test_gene.py",
931
+ "sha256": "fca6758cda81c4b92c228d423f55722999d735db41b5a859e4350b1c134f2985",
932
+ "language": "Python",
933
+ "lines": 154,
934
+ "truncated": false,
935
+ "block": 3,
936
+ "row": 23730
937
+ },
938
+ {
939
+ "path": "software/tests/test_gtex_genotype.py",
940
+ "sha256": "63df79466ecc444e0849f1934392f095d1988e4480bbf875bef155a5612ba037",
941
+ "language": "Python",
942
+ "lines": 90,
943
+ "truncated": false,
944
+ "block": 3,
945
+ "row": 22139
946
+ },
947
+ {
948
+ "path": "software/tests/test_gwas.py",
949
+ "sha256": "6e6f9b9fe2b2d37795665ea4f32b756e695f572faad0ae2dbe229b3892c7f12f",
950
+ "language": "Python",
951
+ "lines": 272,
952
+ "truncated": false,
953
+ "block": 3,
954
+ "row": 25566
955
+ },
956
+ {
957
+ "path": "software/tests/test_gwas_special_handling.py",
958
+ "sha256": "cdd251cc5cfd80f35e2bc9c5707eae5c2183f2e2c523a0560c63e81f47f072d1",
959
+ "language": "Python",
960
+ "lines": 40,
961
+ "truncated": false,
962
+ "block": 3,
963
+ "row": 19500
964
+ },
965
+ {
966
+ "path": "software/tests/test_gwas_utilities.py",
967
+ "sha256": "be62da66c43e81b39eefb71e1c02cbb6450788e4a19225d3b94d67190f590549",
968
+ "language": "Python",
969
+ "lines": 75,
970
+ "truncated": false,
971
+ "block": 3,
972
+ "row": 21720
973
+ },
974
+ {
975
+ "path": "software/tests/test_keyed_data_source.py",
976
+ "sha256": "0bc166c7b0c9b9077f0b6b2b4c6c6ee1e952bd20d395daa17c5e27b101878ff9",
977
+ "language": "Python",
978
+ "lines": 40,
979
+ "truncated": false,
980
+ "block": 3,
981
+ "row": 19355
982
+ },
983
+ {
984
+ "path": "software/tests/test_keyed_dataset.py",
985
+ "sha256": "bec5a88d652f3724fe594e2816180838166a9778bf1ab70cfd22a2d2589c6248",
986
+ "language": "Python",
987
+ "lines": 413,
988
+ "truncated": false,
989
+ "block": 3,
990
+ "row": 26955
991
+ },
992
+ {
993
+ "path": "software/tests/test_matrix_manager.py",
994
+ "sha256": "ea9457b60c43db715902336d2b6b6304542e132f39f84892031814d6641b68a4",
995
+ "language": "Python",
996
+ "lines": 101,
997
+ "truncated": false,
998
+ "block": 3,
999
+ "row": 22157
1000
+ },
1001
+ {
1002
+ "path": "software/tests/test_prediction_model.py",
1003
+ "sha256": "ef876e90b66c19d47e50d92b27ff237dfe38e2076721bbe20417a601a42cba8e",
1004
+ "language": "Python",
1005
+ "lines": 167,
1006
+ "truncated": false,
1007
+ "block": 3,
1008
+ "row": 25046
1009
+ },
1010
+ {
1011
+ "path": "software/tests/test_predixcan_format_utilities.py",
1012
+ "sha256": "f8fa5ad40cac1592b2c2c6d7d024d7018c9eb759b4d38f573ec73b291ecd30be",
1013
+ "language": "Python",
1014
+ "lines": 58,
1015
+ "truncated": false,
1016
+ "block": 3,
1017
+ "row": 20300
1018
+ },
1019
+ {
1020
+ "path": "software/tests/test_thousand_genomes_utilities.py",
1021
+ "sha256": "14265659f94a05a93f0f7acded326f41d1c84d82711a96f37bbce0c0b8d433f3",
1022
+ "language": "Python",
1023
+ "lines": 156,
1024
+ "truncated": false,
1025
+ "block": 3,
1026
+ "row": 23519
1027
+ },
1028
+ {
1029
+ "path": "software/tests/test_utilities.py",
1030
+ "sha256": "5fccd72283789f6363b029a4bee9c3f5d6dc6277a54c6368886e9988f669c17d",
1031
+ "language": "Python",
1032
+ "lines": 235,
1033
+ "truncated": false,
1034
+ "block": 3,
1035
+ "row": 25404
1036
+ },
1037
+ {
1038
+ "path": "software/tests/test_weight_db_utilities.py",
1039
+ "sha256": "ba66dce498c4f66734b035992924042978022d98c86d11e15327b7a7e78aa46e",
1040
+ "language": "Python",
1041
+ "lines": 194,
1042
+ "truncated": false,
1043
+ "block": 3,
1044
+ "row": 24193
1045
+ }
1046
+ ]
1047
+ }
manifests/f2/github.com__nicalab__support.json ADDED
@@ -0,0 +1,147 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/nicalab/support",
4
+ "url": "https://github.com/NICALab/SUPPORT",
5
+ "host": "github.com",
6
+ "commit": "9fba0f415b35106d7d7b9c0144e72917329f0575",
7
+ "license": "GPL-3.0",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986",
14
+ "language": "License",
15
+ "lines": 674,
16
+ "truncated": false,
17
+ "block": 1,
18
+ "row": 2235
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "951f6a5b8247fe0838a32563647acddf2c273b8d2a940083c79bb52eb1cfad0d",
23
+ "language": "Text",
24
+ "lines": 224,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2654
28
+ },
29
+ {
30
+ "path": "colab/functions.py",
31
+ "sha256": "4726d0385905aa1cafd6fb5aeeed1ad77b8d98587054b252c96237c1dc7e6850",
32
+ "language": "Python",
33
+ "lines": 250,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 24889
37
+ },
38
+ {
39
+ "path": "colab/model.py",
40
+ "sha256": "12977299221bcc32340a55b92927ed767d5b78198101673b09fcb3c19756d6b5",
41
+ "language": "Python",
42
+ "lines": 553,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 26899
46
+ },
47
+ {
48
+ "path": "colab/utils.py",
49
+ "sha256": "df598a453718383bf2c931e2c8f626c582f404fa5309695f86340138eb194f40",
50
+ "language": "Python",
51
+ "lines": 362,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 26477
55
+ },
56
+ {
57
+ "path": "model/SUPPORT.py",
58
+ "sha256": "4df5ba356018ae96cbd17bc84179189c049ce6a3a939cbadfc446a30467fc0b1",
59
+ "language": "Python",
60
+ "lines": 450,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 26511
64
+ },
65
+ {
66
+ "path": "model/convhole.py",
67
+ "sha256": "7591cfc7fb26d3d9a8947f463e39ff0ff687800803c4150e3e6e009167784c8f",
68
+ "language": "Python",
69
+ "lines": 131,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 21692
73
+ },
74
+ {
75
+ "path": "src/GUI/test_GUI.py",
76
+ "sha256": "b73b928b78775a2ba77fb894f6a69dea8e2f2561f93e1a3c454aa76244c74c75",
77
+ "language": "Python",
78
+ "lines": 809,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 27584
82
+ },
83
+ {
84
+ "path": "src/GUI/train_GUI.py",
85
+ "sha256": "c6fbf71d5c1d7631be03750d96ece3fc1e00c92833f2c3e5b6768e6def56ff95",
86
+ "language": "Python",
87
+ "lines": 795,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 27544
91
+ },
92
+ {
93
+ "path": "src/test.py",
94
+ "sha256": "18b3215f91bfb93520e4643c57b4054fd455260dad9f29d105cd3aac149e08dd",
95
+ "language": "Python",
96
+ "lines": 82,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 21830
100
+ },
101
+ {
102
+ "path": "src/test_directory.py",
103
+ "sha256": "2e8183b2d316457001a99826aa4f5ba85338cec9997c6abfbace4c16c1bcad74",
104
+ "language": "Python",
105
+ "lines": 115,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 23066
109
+ },
110
+ {
111
+ "path": "src/train.py",
112
+ "sha256": "c632319fcd3615383401b7373972de532fa968f29c2f49b03dd82d824655f9a7",
113
+ "language": "Python",
114
+ "lines": 184,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 24638
118
+ },
119
+ {
120
+ "path": "src/utils/dataset.py",
121
+ "sha256": "aa9114c9bb5a9c240b90476bdd3d868a7977e3038237dcbe2fdec37fb1f29dd0",
122
+ "language": "Python",
123
+ "lines": 306,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 26099
127
+ },
128
+ {
129
+ "path": "src/utils/dataset_pyqt.py",
130
+ "sha256": "84e4e7db7a8f98910507e68e5caa9952de89ba55759b8f4cae8b0dee97df3b5b",
131
+ "language": "Python",
132
+ "lines": 148,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 22701
136
+ },
137
+ {
138
+ "path": "src/utils/util.py",
139
+ "sha256": "4d59b82da07e487e9202ef86046734d2130d629c76553b6dbb8fe9e12a697fd1",
140
+ "language": "Python",
141
+ "lines": 205,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 25507
145
+ }
146
+ ]
147
+ }
manifests/f2/zenodo__14254094.json ADDED
@@ -0,0 +1,129 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:14254094",
4
+ "url": "https://doi.org/10.5281/zenodo.14254094",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "GPL-3.0",
8
+ "license_confirmed_by": "license of the archive's record",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "README.md",
13
+ "sha256": "c1c810ef1addd5c0459fc708832565c57592c9569da96a06e5bfbf7162454e6c",
14
+ "language": "Text",
15
+ "lines": 208,
16
+ "truncated": false,
17
+ "block": 4,
18
+ "row": 2618
19
+ },
20
+ {
21
+ "path": "src/align_photometry_behaviour.py",
22
+ "sha256": "85356033cf1619c08ade8f91f8a01a931c549d9d369fc1a10ee90ba8ffc2b7ae",
23
+ "language": "Python",
24
+ "lines": 3735,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 113
28
+ },
29
+ {
30
+ "path": "src/align_telemetry_opto_photom.py",
31
+ "sha256": "bcc767ef0d4344a2b35cc21937be33c218438f18a451f8c7511c272c4ea03fad",
32
+ "language": "Python",
33
+ "lines": 4576,
34
+ "truncated": true,
35
+ "block": 4,
36
+ "row": 127
37
+ },
38
+ {
39
+ "path": "src/app_dashboard.py",
40
+ "sha256": "3cf20bf605a277143c8045ae418380a62a5065795f1f3b22605366f2dc154aa8",
41
+ "language": "Python",
42
+ "lines": 149,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 23403
46
+ },
47
+ {
48
+ "path": "src/app_settings_manager.py",
49
+ "sha256": "d2cc1d975ed32bb2f0ecfaa6470914ef846b0a9c5b0d7d1e0318a625d837e5bf",
50
+ "language": "Python",
51
+ "lines": 334,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 26409
55
+ },
56
+ {
57
+ "path": "src/behaviour_event_input_frame.py",
58
+ "sha256": "08ec45d79ee0f13d7cf68a231f7c234c46669d03ef8ab2c36141e77a3dd30ee1",
59
+ "language": "Python",
60
+ "lines": 112,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 23060
64
+ },
65
+ {
66
+ "path": "src/combine_data_stats.py",
67
+ "sha256": "3582c97f822c67bda14af9e56f5d9b6b8efc3064b59425e62233986b43239a8f",
68
+ "language": "Python",
69
+ "lines": 1,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 17340
73
+ },
74
+ {
75
+ "path": "src/data_selection_frame.py",
76
+ "sha256": "280a677a899e4682d69e501d7e5fb8515cd12f9eafa460cce929f98afa53d27b",
77
+ "language": "Python",
78
+ "lines": 450,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 26983
82
+ },
83
+ {
84
+ "path": "src/export_options_container.py",
85
+ "sha256": "a7a44c8f99aa52124e11131b1c1d89077fd3e5ea8a71dd5952fa80b2b7b22807",
86
+ "language": "Python",
87
+ "lines": 186,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 24942
91
+ },
92
+ {
93
+ "path": "src/graph_settings_container.py",
94
+ "sha256": "d081b81cab3230a171975f95064e60e5c930f4fe363fbfea8f1ef98dc36a6ec3",
95
+ "language": "Python",
96
+ "lines": 1373,
97
+ "truncated": false,
98
+ "block": 4,
99
+ "row": 1
100
+ },
101
+ {
102
+ "path": "src/main_app.py",
103
+ "sha256": "2176948b4245af288daf930a098f56aa8743602f75caf864c697b23b44619d13",
104
+ "language": "Python",
105
+ "lines": 40,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 19407
109
+ },
110
+ {
111
+ "path": "src/static_inputs_frame.py",
112
+ "sha256": "cd685564a1a2cf286e8d49f1607bac62c99a9e529c3477ac80b988a5f895c158",
113
+ "language": "Python",
114
+ "lines": 86,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 22593
118
+ },
119
+ {
120
+ "path": "src/window_utils.py",
121
+ "sha256": "a919c59ab6a625521bc00a1ef58d6ff41fa63e002ccbd2a94d7b86a931a3f01b",
122
+ "language": "Python",
123
+ "lines": 85,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 20500
127
+ }
128
+ ]
129
+ }
manifests/f2/zenodo__19331923.json ADDED
@@ -0,0 +1,192 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:19331923",
4
+ "url": "10.5281/zenodo.19331923",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "CC-BY-4.0",
8
+ "license_confirmed_by": "license of the archive's record",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "Supportfunction.zip/A_BurstDetect.m",
13
+ "sha256": "2cef4332adf688f5615202287f1669c8df8b9e4477677f4d5e66cc2fa2ffe6a3",
14
+ "language": "MATLAB",
15
+ "lines": 48,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 12454
19
+ },
20
+ {
21
+ "path": "Supportfunction.zip/A_applyfilter_decimate.m",
22
+ "sha256": "bfdc419393040445b44ce05040459847d2483dd0bfae734836aa05638d51050e",
23
+ "language": "MATLAB",
24
+ "lines": 22,
25
+ "truncated": false,
26
+ "block": 3,
27
+ "row": 9470
28
+ },
29
+ {
30
+ "path": "Supportfunction.zip/F_loadPhotometryData.m",
31
+ "sha256": "b14ba033648095462414b0200ba472aee44c0f97f3eccc2c2b9ac9ed540e3989",
32
+ "language": "MATLAB",
33
+ "lines": 67,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 12985
37
+ },
38
+ {
39
+ "path": "Supportfunction.zip/F_openKilosort.m",
40
+ "sha256": "7d189fede079064e8892b5066cdb79b26056a97bbce5e47d03415765d6b5d122",
41
+ "language": "MATLAB",
42
+ "lines": 377,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 16582
46
+ },
47
+ {
48
+ "path": "Supportfunction.zip/F_openNEX.m",
49
+ "sha256": "37e04ba2b983521e2780b4263ebc4e7f6df56e8b0e2474e7fd720320e7aee562",
50
+ "language": "MATLAB",
51
+ "lines": 344,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 16639
55
+ },
56
+ {
57
+ "path": "Supportfunction.zip/F_sort_nat.m",
58
+ "sha256": "da1c41cbb7e4066a5ebe79f8e375e70451641852f1a2c223c88404a74c499b71",
59
+ "language": "MATLAB",
60
+ "lines": 95,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 13418
64
+ },
65
+ {
66
+ "path": "Supportfunction.zip/F_stdshade.m",
67
+ "sha256": "644ef6886d54bec673f9f2d2f15f8ac545dc917f73f394b794a9dd60434161d1",
68
+ "language": "MATLAB",
69
+ "lines": 72,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 11666
73
+ },
74
+ {
75
+ "path": "Supportfunction.zip/load_open_ephys_data.m",
76
+ "sha256": "66d72db0427735897fb999dcc1af138e083dfcefa984f247ef1b12b76101a34e",
77
+ "language": "MATLAB",
78
+ "lines": 643,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 16872
82
+ },
83
+ {
84
+ "path": "Supportfunction.zip/openOpE.m",
85
+ "sha256": "07dbee1231b9aec60511bfee61a2512481689d3b15c61cce0e929374c16c19d5",
86
+ "language": "MATLAB",
87
+ "lines": 1449,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 17175
91
+ },
92
+ {
93
+ "path": "Supportfunction.zip/readNPY.m",
94
+ "sha256": "1ba677a4cc68708d5d79ab93770be7f735ecaf46cd00e35df810bb60599f5958",
95
+ "language": "MATLAB",
96
+ "lines": 36,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 9952
100
+ },
101
+ {
102
+ "path": "f3_IPS.zip/a01_EphyReplot_acrossSU_SM_IPS.m",
103
+ "sha256": "37b05b35a9bf8cdf9c74b6a3c224e952c3c92d50b11bc47aefacb7a64da848d2",
104
+ "language": "MATLAB",
105
+ "lines": 370,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 16498
109
+ },
110
+ {
111
+ "path": "f3_IPS.zip/a02_EphyReplot_acrossSU_SM_IPSplot3D.m",
112
+ "sha256": "9c7f43b60f72bef8785c2c85a4e0b7575c1d4166aced3e6d2fc0310366b185fb",
113
+ "language": "MATLAB",
114
+ "lines": 83,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 12180
118
+ },
119
+ {
120
+ "path": "s1_ModelingQRPE.zip/a01_RawDataCompiler.m",
121
+ "sha256": "68764811a7181ced62e8b6f033c58fadcd8cbb1ceaac1f1d087496e4f263aa2e",
122
+ "language": "MATLAB",
123
+ "lines": 116,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 14139
127
+ },
128
+ {
129
+ "path": "s1_ModelingQRPE.zip/a02_hBayesDM_prl_Lu.R",
130
+ "sha256": "8f8e7460374bf420e3d6678c68b9ac7bfc4633348e7afa54a4ebedb2459d26e0",
131
+ "language": "R",
132
+ "lines": 103,
133
+ "truncated": false,
134
+ "block": 4,
135
+ "row": 612
136
+ },
137
+ {
138
+ "path": "s1_ModelingQRPE.zip/a03_ModelReader.m",
139
+ "sha256": "f6f4ac34215364cbb750bd45e1dd343c8cb8726442f385522c319c52580730d9",
140
+ "language": "MATLAB",
141
+ "lines": 419,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 16682
145
+ },
146
+ {
147
+ "path": "s8_VectorStrength.zip/A_SpikeVectorStrength_Plot.m",
148
+ "sha256": "46bec22a506a18b1be25037e4dc4bee15e3edd92b23cfe33bccc436657403a9c",
149
+ "language": "MATLAB",
150
+ "lines": 66,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 12529
154
+ },
155
+ {
156
+ "path": "s8_VectorStrength.zip/B_SpikeVectorStrength_Statistic.m",
157
+ "sha256": "28806d111c07d21107311eec7416477fbc40be0958030bfaba5dd382655a591f",
158
+ "language": "MATLAB",
159
+ "lines": 106,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 12955
163
+ },
164
+ {
165
+ "path": "s9_ML.zip/A02_Read_decoding_outcome.m",
166
+ "sha256": "1cdcaf77750cc1d8841511a0ee8d4268ac9cf34ebcdedf620c66760af0f5055d",
167
+ "language": "MATLAB",
168
+ "lines": 147,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 14560
172
+ },
173
+ {
174
+ "path": "s9_ML.zip/DCN/DCNdecodingSVM.py",
175
+ "sha256": "725850c9866ae6692e62a0652f8a14ca56fb52fd641d673d19d7c0f58a5fe300",
176
+ "language": "Python",
177
+ "lines": 119,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 22566
181
+ },
182
+ {
183
+ "path": "s9_ML.zip/VTA/VTAdecodingSVM.py",
184
+ "sha256": "88728fb79b203dc12ac8085d812b2a172cc53e0d78943130220a0c195ddf2a50",
185
+ "language": "Python",
186
+ "lines": 117,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 22551
190
+ }
191
+ ]
192
+ }
manifests/f3/github.com__dicemt__dti-noddi.json ADDED
@@ -0,0 +1,57 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/dicemt/dti-noddi",
4
+ "url": "https://github.com/dicemt/DTI-NODDI",
5
+ "host": "github.com",
6
+ "commit": "cb9cadd0f7c20d5cb2083aa5f9f8c14c13a9cd58",
7
+ "license": "AGPL-3.0",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "7f8f48e4266aa8fd3033dfaa4bb7f6e83a60c6e099f82d4959b81de90e67cd8f",
14
+ "language": "License",
15
+ "lines": 661,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8165
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "eef11108de58278ead1020add2677f6bdb616b96e36e3d9dd84184b56d5b8f32",
23
+ "language": "Text",
24
+ "lines": 74,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2453
28
+ },
29
+ {
30
+ "path": "dti_noddi.py",
31
+ "sha256": "62b827e4a8ca8efb254d6cbccdd9c48cda85fc1e0a40a0e88af83b5502d20741",
32
+ "language": "Python",
33
+ "lines": 122,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 21629
37
+ },
38
+ {
39
+ "path": "dti_noddi_api.py",
40
+ "sha256": "1c56ae201ac8da1e485d7b1215e5d235eb48a75a8ae9e2f6ad7729c053695381",
41
+ "language": "Python",
42
+ "lines": 135,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 21989
46
+ },
47
+ {
48
+ "path": "dti_noddi_fit.py",
49
+ "sha256": "5247ae6b4fceec5e8c6f8d4842ef5ea2e1567d1025c530b6dda86c0b3d8d6279",
50
+ "language": "Python",
51
+ "lines": 56,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 19832
55
+ }
56
+ ]
57
+ }
manifests/f3/zenodo__15095228.json ADDED
@@ -0,0 +1,111 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:15095228",
4
+ "url": "10.5281/zenodo.15095228",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "GPL-3.0",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "Download_Dataset.sh",
13
+ "sha256": "1c07a94ef38e8925b0b9a6becc01a14d92715e11b01e0280bf7f611d336a6658",
14
+ "language": "Shell",
15
+ "lines": 15,
16
+ "truncated": false,
17
+ "block": 4,
18
+ "row": 1624
19
+ },
20
+ {
21
+ "path": "LICENSE",
22
+ "sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986",
23
+ "language": "License",
24
+ "lines": 674,
25
+ "truncated": false,
26
+ "block": 1,
27
+ "row": 2235
28
+ },
29
+ {
30
+ "path": "README.md",
31
+ "sha256": "7e94e3ef1b3f7afcca87da8a7e0967b68d2a933a415d66fb8ea5c86e47b10efd",
32
+ "language": "Text",
33
+ "lines": 204,
34
+ "truncated": false,
35
+ "block": 4,
36
+ "row": 2707
37
+ },
38
+ {
39
+ "path": "code/calculate_gain.py",
40
+ "sha256": "c1361dd636c280176c4fac32511f967df38e490be2bbc7fd7d64e1e59058caab",
41
+ "language": "Python",
42
+ "lines": 180,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 24036
46
+ },
47
+ {
48
+ "path": "code/main.py",
49
+ "sha256": "8721331f85836ffd53fc5e911a0002e9c64a5c0608b7dfc576d95598982a73c5",
50
+ "language": "Python",
51
+ "lines": 148,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 24349
55
+ },
56
+ {
57
+ "path": "code/optunaTuningUnix.py",
58
+ "sha256": "78b94f58b3d729395c3a0ee9769309138afb2989f73880b1e254ea03ef33207a",
59
+ "language": "Python",
60
+ "lines": 210,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 25119
64
+ },
65
+ {
66
+ "path": "code/optunaTuningWindows.py",
67
+ "sha256": "a3a0de661810175054a38c275bb6eb3252f579b311909c78eb80132718a5953d",
68
+ "language": "Python",
69
+ "lines": 211,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 25159
73
+ },
74
+ {
75
+ "path": "code/precision.py",
76
+ "sha256": "4f70c403c7520aa329aa6f142715ad4e34d869a5914992dae2f88be1039bad33",
77
+ "language": "Python",
78
+ "lines": 145,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 23385
82
+ },
83
+ {
84
+ "path": "code/pretrained.py",
85
+ "sha256": "59ab71fe9534b162d62df20916345ba2831078ad8e88f1b89c4c06d9402f7fd1",
86
+ "language": "Python",
87
+ "lines": 31,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 19151
91
+ },
92
+ {
93
+ "path": "code/train.py",
94
+ "sha256": "2d1b45840579f3d70b36cf7bca6640a45cb006111a9c5e0475535f1b660ab37c",
95
+ "language": "Python",
96
+ "lines": 32,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 19437
100
+ },
101
+ {
102
+ "path": "code/utilities.py",
103
+ "sha256": "969d2c714c6645efd6fb6f82b73d5a2eb4d3a9ab63da23ef0162ce9b57b08888",
104
+ "language": "Python",
105
+ "lines": 269,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 25034
109
+ }
110
+ ]
111
+ }
manifests/f5/github.com__jlhos-fmri__clinicalfrequencyanalysistoolkit.json ADDED
@@ -0,0 +1,228 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/jlhos-fmri/clinicalfrequencyanalysistoolkit",
4
+ "url": "https://github.com/JLhos-fmri/ClinicalFrequencyAnalysisToolkit",
5
+ "host": "github.com",
6
+ "commit": "8fcc568032378fc1709f4a01bfe7fae6bc99b025",
7
+ "license": "GPL-3.0",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "CFAT.m",
13
+ "sha256": "9d609a8d8114c0e9943f54c5532a64e736325e69516e248d19bf800ac957908c",
14
+ "language": "MATLAB",
15
+ "lines": 114,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 13518
19
+ },
20
+ {
21
+ "path": "CFA_Checkandrun.m",
22
+ "sha256": "31ab5445548f95f6b69cca0dcdf2228880c812051061bb91b12532a9a260c091",
23
+ "language": "MATLAB",
24
+ "lines": 366,
25
+ "truncated": false,
26
+ "block": 3,
27
+ "row": 16317
28
+ },
29
+ {
30
+ "path": "CFA_MakeRes.m",
31
+ "sha256": "a13715805c74a6966ad429d101900590eab53e01358255fa641de5aedc22c9a3",
32
+ "language": "MATLAB",
33
+ "lines": 778,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 17182
37
+ },
38
+ {
39
+ "path": "CFA_ReOrient_Single.m",
40
+ "sha256": "96fffd0c82f249ab79c1aad4b4d0a356e6173d083e7d32463b7acbec112e3c89",
41
+ "language": "MATLAB",
42
+ "lines": 30,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 10232
46
+ },
47
+ {
48
+ "path": "CFA_ReOrient_Twomode.m",
49
+ "sha256": "3c2b025b8763eaccef8a83a5b6787150d4f03fa02bb478c8e856fe8555d57073",
50
+ "language": "MATLAB",
51
+ "lines": 55,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 11850
55
+ },
56
+ {
57
+ "path": "CFA_RunAllJob.m",
58
+ "sha256": "f46ab27e9d4f612c0b7dd15d85da989c8e54dd256fb4a052b75cb4e98425f1c3",
59
+ "language": "MATLAB",
60
+ "lines": 246,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 16090
64
+ },
65
+ {
66
+ "path": "CFA_SingleGroupPval_Perm.m",
67
+ "sha256": "a28e714d472899154475e4187b283e6507b274213c287742ad3cffc5bf7cf2df",
68
+ "language": "MATLAB",
69
+ "lines": 55,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 11804
73
+ },
74
+ {
75
+ "path": "CFA_inout.m",
76
+ "sha256": "175bca04c25c1d6879d2c072668c25692b04714bc5c6e70e73bc3fad5c601396",
77
+ "language": "MATLAB",
78
+ "lines": 756,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 16983
82
+ },
83
+ {
84
+ "path": "CFA_template.m",
85
+ "sha256": "ff102d2c6cb33521f5ed0b6ac76daee71bab464210cf88d3dc7d4055c06b4884",
86
+ "language": "MATLAB",
87
+ "lines": 428,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 16591
91
+ },
92
+ {
93
+ "path": "ClincFreq_CalHeatNum.m",
94
+ "sha256": "46866bfb52d12513ef120a578450555800d4b46571fefc592eb357df0427b834",
95
+ "language": "MATLAB",
96
+ "lines": 95,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 14689
100
+ },
101
+ {
102
+ "path": "ClincFreq_HeatNumStat.m",
103
+ "sha256": "b75e9dac75f6c28d9f158574e11cae1595fef7a7ec2fd764925f55367181079f",
104
+ "language": "MATLAB",
105
+ "lines": 376,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 16952
109
+ },
110
+ {
111
+ "path": "ClincFreq_Norm2MNI_CT_clinc.m",
112
+ "sha256": "1f3105f36f87800d5b3ca8ed45085e336babe8fa7fba98ba6b138ad8031765e2",
113
+ "language": "MATLAB",
114
+ "lines": 26,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 10203
118
+ },
119
+ {
120
+ "path": "ClincFreq_Norm2MNI_EPI.m",
121
+ "sha256": "050a7d1bab2702cf76e57b6b94256c62e38139ffca548075ef0df91dbc865125",
122
+ "language": "MATLAB",
123
+ "lines": 38,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 12079
127
+ },
128
+ {
129
+ "path": "ClincFreq_Norm2MNI_T1_clinc.m",
130
+ "sha256": "a9ed0753b8ab57aca2d9e1059761c0cc1d5e8425d2828599b7df60c5c71d3fb7",
131
+ "language": "MATLAB",
132
+ "lines": 22,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 10021
136
+ },
137
+ {
138
+ "path": "ClincFreq_Norm2MNI_T2.m",
139
+ "sha256": "36ebf09f724e738a6c673b1c324ee592eefce518d6659ff5f3f3d86ec239718e",
140
+ "language": "MATLAB",
141
+ "lines": 38,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 12076
145
+ },
146
+ {
147
+ "path": "ClincFreq_Norm2MNI_withT1_clinc.m",
148
+ "sha256": "88fa2b375ced0ad9cf6eb374b7be4847661c81eb4d341580e745101783cb9d66",
149
+ "language": "MATLAB",
150
+ "lines": 30,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 10787
154
+ },
155
+ {
156
+ "path": "DynamicBC_write_NIFTI.m",
157
+ "sha256": "bc5b78e83ddead18886171e18478d91ba60f72d9132868033417e0462053f77e",
158
+ "language": "MATLAB",
159
+ "lines": 19,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 8955
163
+ },
164
+ {
165
+ "path": "Dynamic_read_dir_NIFTI.m",
166
+ "sha256": "bdbd2ba1cc72b682d5efdc0762680abddad3ab2ffeb868904c74094d9a9e61c1",
167
+ "language": "MATLAB",
168
+ "lines": 45,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 10803
172
+ },
173
+ {
174
+ "path": "Dynamic_read_dir_NIFTI_sparse.m",
175
+ "sha256": "1a6e4a85cf990f6c414a543729a930a563a391f71057644dba09bc6ba99ebafe",
176
+ "language": "MATLAB",
177
+ "lines": 46,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 10915
181
+ },
182
+ {
183
+ "path": "LICENSE",
184
+ "sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986",
185
+ "language": "License",
186
+ "lines": 674,
187
+ "truncated": false,
188
+ "block": 1,
189
+ "row": 2235
190
+ },
191
+ {
192
+ "path": "PermClusterInfo.m",
193
+ "sha256": "8b431aa1a461abad4bd0d1cad7243b49dfe5b022369dd43d6728a7ec95a9ce18",
194
+ "language": "MATLAB",
195
+ "lines": 40,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 9628
199
+ },
200
+ {
201
+ "path": "dynamicBC_Reslice.m",
202
+ "sha256": "90b55e8ef879e759cea378082c96965685dea9d1deaf592a77d0cc98f5065e1a",
203
+ "language": "MATLAB",
204
+ "lines": 60,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 12806
208
+ },
209
+ {
210
+ "path": "getclusterinfo.m",
211
+ "sha256": "7557bf08383f7f5fc07bb66b3f195190a10d30442308737221e025a7a226383b",
212
+ "language": "MATLAB",
213
+ "lines": 63,
214
+ "truncated": false,
215
+ "block": 3,
216
+ "row": 11276
217
+ },
218
+ {
219
+ "path": "getinfomat.m",
220
+ "sha256": "5f64695557e994d6f9f856d3817c684622b6b0f2f9bb4265af1ce3c9bc1d5b31",
221
+ "language": "MATLAB",
222
+ "lines": 9,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 8407
226
+ }
227
+ ]
228
+ }
manifests/f5/zenodo__8018820.json ADDED
@@ -0,0 +1,1002 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:8018820",
4
+ "url": "https://zenodo.org/record/8018820",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "Extract_BB_Responses_2SD_MK.m",
13
+ "sha256": "fef6df7ef6ba83ef36de5eeb1dd6224cdc434be94167b1dc914bced7786abecd",
14
+ "language": "MATLAB",
15
+ "lines": 309,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 16294
19
+ },
20
+ {
21
+ "path": "FISSAscript_MK.py",
22
+ "sha256": "f041c05493b61d5d312c4206255f0e9d64dba430dab3fe3dc97f283d7722709d",
23
+ "language": "Python",
24
+ "lines": 75,
25
+ "truncated": false,
26
+ "block": 3,
27
+ "row": 21062
28
+ },
29
+ {
30
+ "path": "GUIs/meanfluoROIvtGUI.m",
31
+ "sha256": "afcce33043dc8cb8dbfa13f552d8e69ece1eed7504b72446b521da5f10eab6cd",
32
+ "language": "MATLAB",
33
+ "lines": 1733,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 17240
37
+ },
38
+ {
39
+ "path": "GUIs/minimalTifROIgui.m",
40
+ "sha256": "6c0d099c50c78868075c91f7ff98527a274f523a6c22bd4b7edb0e23a5f94446",
41
+ "language": "MATLAB",
42
+ "lines": 543,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 16937
46
+ },
47
+ {
48
+ "path": "GUIs/normCorreTifROIgui.m",
49
+ "sha256": "d783685dc55b3687d3e4ba28871a0ea059223b6b47d0aaa23972e499ea280b92",
50
+ "language": "MATLAB",
51
+ "lines": 516,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 16910
55
+ },
56
+ {
57
+ "path": "GUIs/roiGUI.m",
58
+ "sha256": "74fa7a9552855a98a31f32d72b29a66f10ba578d082d324b4021408337eb982b",
59
+ "language": "MATLAB",
60
+ "lines": 1191,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 17189
64
+ },
65
+ {
66
+ "path": "LICENSE",
67
+ "sha256": "70e87b030b8f84e0c381ccba6f9212f49a9c9402082bbe2653a37da73afd2265",
68
+ "language": "License",
69
+ "lines": 21,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 8062
73
+ },
74
+ {
75
+ "path": "NoRMCorre/@MotionCorrection/MotionCorrection.m",
76
+ "sha256": "6e217a0f2e01be0bc4474aa54d6efd54dbc1d0223c92ba9b168cfe14d930b7c6",
77
+ "language": "MATLAB",
78
+ "lines": 209,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 16186
82
+ },
83
+ {
84
+ "path": "NoRMCorre/NoRMCorreSetParms.m",
85
+ "sha256": "202bf97e0bf01393a4c9de8717479ae76084e92088da89105b5bf3dafbf4af4e",
86
+ "language": "MATLAB",
87
+ "lines": 235,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 16338
91
+ },
92
+ {
93
+ "path": "NoRMCorre/apply_shifts.m",
94
+ "sha256": "7dc649462581a864f7c223f7e258eb85009bfe1f9184f8e0eeabdded3196ce97",
95
+ "language": "MATLAB",
96
+ "lines": 306,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 16494
100
+ },
101
+ {
102
+ "path": "NoRMCorre/bigread2.m",
103
+ "sha256": "4e6196f952eb2a0ab01529f297981906de09c006ebd5417ac99b8a77f749a1da",
104
+ "language": "MATLAB",
105
+ "lines": 173,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 15183
109
+ },
110
+ {
111
+ "path": "NoRMCorre/cell2mat_ov.m",
112
+ "sha256": "538c5b9cbfa3b97ad8cf4f3755a997f47df2b252d8e044bc8cdb7e1e97e4d7e3",
113
+ "language": "MATLAB",
114
+ "lines": 27,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 10418
118
+ },
119
+ {
120
+ "path": "NoRMCorre/cell2mat_ov_sum.m",
121
+ "sha256": "86422bed0a29f326f5865717ded01f10795c8e1c89051757c1222b0b9ab50bce",
122
+ "language": "MATLAB",
123
+ "lines": 42,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 12496
127
+ },
128
+ {
129
+ "path": "NoRMCorre/concatenate_files.m",
130
+ "sha256": "0d2e45b18a148712c153b86f5db863c33969d73e74ef9ee6fa44b5b870d3bce7",
131
+ "language": "MATLAB",
132
+ "lines": 57,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 11750
136
+ },
137
+ {
138
+ "path": "NoRMCorre/construct_grid.m",
139
+ "sha256": "762f94c078f64f111b92a5686e0c4153c0a4509bb2bf064046db4496269b81b1",
140
+ "language": "MATLAB",
141
+ "lines": 33,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 10216
145
+ },
146
+ {
147
+ "path": "NoRMCorre/construct_grid_even.m",
148
+ "sha256": "b912d004e981a769c00921c3a271188143d39e94d70bb416d641ab04485c2c22",
149
+ "language": "MATLAB",
150
+ "lines": 28,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 9716
154
+ },
155
+ {
156
+ "path": "NoRMCorre/construct_weights.m",
157
+ "sha256": "187dedc1733e64e1e8de917b6994e2e220ed5ac2688f404fe9f812af9e45a10a",
158
+ "language": "MATLAB",
159
+ "lines": 8,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 9656
163
+ },
164
+ {
165
+ "path": "NoRMCorre/correct_bidirectional_offset.m",
166
+ "sha256": "eb110b8b2f84c7b661d98b8bf3a22d3d93a180abe0cfbf510fc57636792647f2",
167
+ "language": "MATLAB",
168
+ "lines": 77,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 12417
172
+ },
173
+ {
174
+ "path": "NoRMCorre/demo.m",
175
+ "sha256": "12136d9bcfdf3581e0d50cd7e4c2b71dcf6cf4eb0da0d8debe9b3d567881aa8d",
176
+ "language": "MATLAB",
177
+ "lines": 82,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 14339
181
+ },
182
+ {
183
+ "path": "NoRMCorre/demo_1p.m",
184
+ "sha256": "6a2b72b0fc93f98be1b403d7e31ab93521e35ba1c1af0b3aa18dd91bd48ffd7c",
185
+ "language": "MATLAB",
186
+ "lines": 172,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 15582
190
+ },
191
+ {
192
+ "path": "NoRMCorre/demo_1p_low_RAM.m",
193
+ "sha256": "ad7743f8bc9e5d39524794b44cc2a7e3f05a53f90b98a56f8f6ceca22c009b98",
194
+ "language": "MATLAB",
195
+ "lines": 62,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 12652
199
+ },
200
+ {
201
+ "path": "NoRMCorre/demo_mc_class.m",
202
+ "sha256": "ffbb5681c96b0ee35b50ad0a4b0e9d6d7b0b820ab09ca181eb08a19c8158a197",
203
+ "language": "MATLAB",
204
+ "lines": 86,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 14387
208
+ },
209
+ {
210
+ "path": "NoRMCorre/dftregistration_min_max.m",
211
+ "sha256": "10c024244f93cbd6feb9feda6dc43e4986479e342d57f5f02c4a3992de9dfe4d",
212
+ "language": "MATLAB",
213
+ "lines": 283,
214
+ "truncated": false,
215
+ "block": 3,
216
+ "row": 16359
217
+ },
218
+ {
219
+ "path": "NoRMCorre/dftregistration_min_max_3d.m",
220
+ "sha256": "8fadfab20c7be5e19221550c435084a36a534124f99fea3445dd2a5dff70ff1b",
221
+ "language": "MATLAB",
222
+ "lines": 315,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 16514
226
+ },
227
+ {
228
+ "path": "NoRMCorre/downsample_data.m",
229
+ "sha256": "9469ff5140236b294ed95a87357182d43b5f9dadd9b180047bbf3e9391c85ba4",
230
+ "language": "MATLAB",
231
+ "lines": 62,
232
+ "truncated": false,
233
+ "block": 3,
234
+ "row": 12816
235
+ },
236
+ {
237
+ "path": "NoRMCorre/h5_2_bin.m",
238
+ "sha256": "abad9d03ca466f8dc3b835d0877a1eaacb1ae99b535ea172671c25efadcea391",
239
+ "language": "MATLAB",
240
+ "lines": 26,
241
+ "truncated": false,
242
+ "block": 3,
243
+ "row": 9414
244
+ },
245
+ {
246
+ "path": "NoRMCorre/han.m",
247
+ "sha256": "0103424a249e57b1b231b26865465192dee4143da5c6eab357f6b06847b0babe",
248
+ "language": "MATLAB",
249
+ "lines": 22,
250
+ "truncated": false,
251
+ "block": 3,
252
+ "row": 9707
253
+ },
254
+ {
255
+ "path": "NoRMCorre/loadtiff.m",
256
+ "sha256": "a05d0d1ff93ea57c7a67eaf41daa59e97b39ff85bb1ec792ebae118ed7acaf0a",
257
+ "language": "MATLAB",
258
+ "lines": 154,
259
+ "truncated": false,
260
+ "block": 3,
261
+ "row": 15103
262
+ },
263
+ {
264
+ "path": "NoRMCorre/loadtiff_old.m",
265
+ "sha256": "a3c20f5f1fa8826952041b9fb6e703b24f8ebbd1d8477ab60c4d395519d5037d",
266
+ "language": "MATLAB",
267
+ "lines": 150,
268
+ "truncated": false,
269
+ "block": 3,
270
+ "row": 14899
271
+ },
272
+ {
273
+ "path": "NoRMCorre/mat2cell_ov.m",
274
+ "sha256": "c8c6bcc3164f93f1c08a90bd6c41822dde1032e5ca88aa6e693aec1c75fdce78",
275
+ "language": "MATLAB",
276
+ "lines": 29,
277
+ "truncated": false,
278
+ "block": 3,
279
+ "row": 10393
280
+ },
281
+ {
282
+ "path": "NoRMCorre/motion_metrics.m",
283
+ "sha256": "902ac59b8a8552fca548d7769c8ad95e32a137fefa2ca03c04bed71bf21f7795",
284
+ "language": "MATLAB",
285
+ "lines": 113,
286
+ "truncated": false,
287
+ "block": 3,
288
+ "row": 13914
289
+ },
290
+ {
291
+ "path": "NoRMCorre/normcorre.m",
292
+ "sha256": "8288e66c14d5939d259d6ce630df82950f105b1692851a3b81e5983b77c8878f",
293
+ "language": "MATLAB",
294
+ "lines": 536,
295
+ "truncated": false,
296
+ "block": 3,
297
+ "row": 17019
298
+ },
299
+ {
300
+ "path": "NoRMCorre/normcorre_batch.m",
301
+ "sha256": "fd0e821e14692651dee7b9985288cee4e24ed5acbf650fdeef1e19ce983792fa",
302
+ "language": "MATLAB",
303
+ "lines": 486,
304
+ "truncated": false,
305
+ "block": 3,
306
+ "row": 16956
307
+ },
308
+ {
309
+ "path": "NoRMCorre/normcorre_batch_even.m",
310
+ "sha256": "92d3f36c605a7dfa93dc36c07621774db61628fa62bce9263a181ed715cd14e9",
311
+ "language": "MATLAB",
312
+ "lines": 330,
313
+ "truncated": false,
314
+ "block": 3,
315
+ "row": 16458
316
+ },
317
+ {
318
+ "path": "NoRMCorre/read_file.m",
319
+ "sha256": "e2b80705fba0a5855c156becbc0e8c79f0b8a9b5f6ec18885a16b02ec12cdcb3",
320
+ "language": "MATLAB",
321
+ "lines": 89,
322
+ "truncated": false,
323
+ "block": 3,
324
+ "row": 13633
325
+ },
326
+ {
327
+ "path": "NoRMCorre/read_raw_file.m",
328
+ "sha256": "ce1252a94e049b9307319683311f4b8686bcf06901cd2f1630718fb874823b99",
329
+ "language": "MATLAB",
330
+ "lines": 27,
331
+ "truncated": false,
332
+ "block": 3,
333
+ "row": 10183
334
+ },
335
+ {
336
+ "path": "NoRMCorre/refreshdisp.m",
337
+ "sha256": "146f1db5a43fefc5786d3b0db7e9b873eee2b0f7d580de6adbf634d8712a4b5e",
338
+ "language": "MATLAB",
339
+ "lines": 12,
340
+ "truncated": false,
341
+ "block": 3,
342
+ "row": 8313
343
+ },
344
+ {
345
+ "path": "NoRMCorre/register_frame.m",
346
+ "sha256": "d4f0e490944344c6b7262662437882728e8245cb0ac4a8933eedd508287451ce",
347
+ "language": "MATLAB",
348
+ "lines": 65,
349
+ "truncated": false,
350
+ "block": 3,
351
+ "row": 13317
352
+ },
353
+ {
354
+ "path": "NoRMCorre/remove_boundaries.m",
355
+ "sha256": "b167a607e42cee568ad1e334f5ed0cfc02ec5371d3e003f522dc436480475089",
356
+ "language": "MATLAB",
357
+ "lines": 40,
358
+ "truncated": false,
359
+ "block": 3,
360
+ "row": 11983
361
+ },
362
+ {
363
+ "path": "NoRMCorre/saveash5.m",
364
+ "sha256": "60f52d0b565b8000cee6737e2828955a056edaafec10c3c8c17f15bf3126a511",
365
+ "language": "MATLAB",
366
+ "lines": 36,
367
+ "truncated": false,
368
+ "block": 3,
369
+ "row": 11099
370
+ },
371
+ {
372
+ "path": "NoRMCorre/saveastiff.m",
373
+ "sha256": "70c3e53c6f085f8526cb4ca0d6bb56d0e10599d6f5981fa4643867e37dd43b28",
374
+ "language": "MATLAB",
375
+ "lines": 304,
376
+ "truncated": false,
377
+ "block": 3,
378
+ "row": 16426
379
+ },
380
+ {
381
+ "path": "NoRMCorre/savefast.m",
382
+ "sha256": "7a2e3a1c48dedb94b441cc3dfafb72ebf44818c50e5029126a7ad71cb31aa17f",
383
+ "language": "MATLAB",
384
+ "lines": 70,
385
+ "truncated": false,
386
+ "block": 3,
387
+ "row": 11993
388
+ },
389
+ {
390
+ "path": "NoRMCorre/shift_reconstruct.m",
391
+ "sha256": "5abebf9b11a507951a3114beccb1400b421a0fcd6700c1d57b9fccc0a8729975",
392
+ "language": "MATLAB",
393
+ "lines": 57,
394
+ "truncated": false,
395
+ "block": 3,
396
+ "row": 11586
397
+ },
398
+ {
399
+ "path": "NoRMCorre/split_frame.m",
400
+ "sha256": "ff02e0fa58762ae4f3b01af60cff4ff268710fd0f6e82fe240698e58e0158ce7",
401
+ "language": "MATLAB",
402
+ "lines": 14,
403
+ "truncated": false,
404
+ "block": 3,
405
+ "row": 8735
406
+ },
407
+ {
408
+ "path": "NoRMCorreFISSApipeline_MK.m",
409
+ "sha256": "bd83a665ab4873556a0f21f54461d7ee67b41d9425a5bf10ee7e2270a03341d4",
410
+ "language": "MATLAB",
411
+ "lines": 349,
412
+ "truncated": false,
413
+ "block": 3,
414
+ "row": 16598
415
+ },
416
+ {
417
+ "path": "fissa/docs/conf.py",
418
+ "sha256": "fa5e563e1209d7f9b7c709a2bcbad2cef292642a94adc90d05f4c58755a77cbe",
419
+ "language": "Python",
420
+ "lines": 265,
421
+ "truncated": false,
422
+ "block": 3,
423
+ "row": 24557
424
+ },
425
+ {
426
+ "path": "fissa/examples/Basic usage.ipynb",
427
+ "sha256": "1c774f5720c4f97359c3ece7eb850d973a51434410ec5dbd9db3ff6c9dd6d0fd",
428
+ "language": "Jupyter",
429
+ "lines": 340,
430
+ "truncated": false,
431
+ "block": 3,
432
+ "row": 7642
433
+ },
434
+ {
435
+ "path": "fissa/examples/SIMA example.ipynb",
436
+ "sha256": "3209e98c56a37a3059ee2bd6830004447ec44b2084ebaef828786a0f1df85c5c",
437
+ "language": "Jupyter",
438
+ "lines": 157,
439
+ "truncated": false,
440
+ "block": 3,
441
+ "row": 7267
442
+ },
443
+ {
444
+ "path": "fissa/examples/Suite2p example.ipynb",
445
+ "sha256": "b3607cca36e3d4dff7a8113c7a71d276d8005eee50936e05b3e2911668296860",
446
+ "language": "Jupyter",
447
+ "lines": 161,
448
+ "truncated": false,
449
+ "block": 3,
450
+ "row": 7375
451
+ },
452
+ {
453
+ "path": "fissa/examples/basic_usage.py",
454
+ "sha256": "7e17b15d6803d084f2023d640b2381a04e6f958e5c74717f83560d8889693cbd",
455
+ "language": "Python",
456
+ "lines": 28,
457
+ "truncated": false,
458
+ "block": 3,
459
+ "row": 18686
460
+ },
461
+ {
462
+ "path": "fissa/examples/basic_usage_windows.py",
463
+ "sha256": "3459d9df62e2ab27d9d104052c71b4896d951a68cad72bf989bb82740858f9f4",
464
+ "language": "Python",
465
+ "lines": 32,
466
+ "truncated": false,
467
+ "block": 3,
468
+ "row": 19008
469
+ },
470
+ {
471
+ "path": "fissa/examples/cNMF example.ipynb",
472
+ "sha256": "53fb956dad82fa263d1f5ade8b47081de28fc1ed5383fc55c66911727c87ea5a",
473
+ "language": "Jupyter",
474
+ "lines": 148,
475
+ "truncated": false,
476
+ "block": 3,
477
+ "row": 7318
478
+ },
479
+ {
480
+ "path": "fissa/examples/datahandler_custom.py",
481
+ "sha256": "01ff7098c342fda86a1eeaeb414be414c438d4bb937c348f07b49b99daffc706",
482
+ "language": "Python",
483
+ "lines": 118,
484
+ "truncated": false,
485
+ "block": 3,
486
+ "row": 21122
487
+ },
488
+ {
489
+ "path": "fissa/fissa/ROI.py",
490
+ "sha256": "831ea0157e69bea1203f9cedd2b3fce2b85293321773bcf6babd0005aa47f85f",
491
+ "language": "Python",
492
+ "lines": 147,
493
+ "truncated": false,
494
+ "block": 3,
495
+ "row": 23059
496
+ },
497
+ {
498
+ "path": "fissa/fissa/__init__.py",
499
+ "sha256": "877c1396569daf32f1332b87a3d0ca48e438927241d857abd84a28ae777d61ce",
500
+ "language": "Python",
501
+ "lines": 5,
502
+ "truncated": false,
503
+ "block": 3,
504
+ "row": 17492
505
+ },
506
+ {
507
+ "path": "fissa/fissa/__meta__.py",
508
+ "sha256": "015eedddc503366e9ae89b4e7314d290ecbb39a3f32945b644e512b9f43bc1c7",
509
+ "language": "Python",
510
+ "lines": 7,
511
+ "truncated": false,
512
+ "block": 3,
513
+ "row": 17783
514
+ },
515
+ {
516
+ "path": "fissa/fissa/core.py",
517
+ "sha256": "9ebbf7181e82ac8606bedaa9b809a2460a1cf78d6ad3708e50046f9a514e58ee",
518
+ "language": "Python",
519
+ "lines": 627,
520
+ "truncated": false,
521
+ "block": 3,
522
+ "row": 27299
523
+ },
524
+ {
525
+ "path": "fissa/fissa/datahandler.py",
526
+ "sha256": "3aae1ff9b64392e0d5c50611c78426cc5b6f8b933b7281226f8f8a91be80cfb7",
527
+ "language": "Python",
528
+ "lines": 130,
529
+ "truncated": false,
530
+ "block": 3,
531
+ "row": 21480
532
+ },
533
+ {
534
+ "path": "fissa/fissa/datahandler_framebyframe.py",
535
+ "sha256": "759a86daeecc21daa0fd0b9a9ea13a943d886bbd5ad096f975b1b1c38ccbb8ce",
536
+ "language": "Python",
537
+ "lines": 153,
538
+ "truncated": false,
539
+ "block": 3,
540
+ "row": 22150
541
+ },
542
+ {
543
+ "path": "fissa/fissa/deltaf.py",
544
+ "sha256": "122ca57b85b28ab714e2f3d86b0fde3ca01879f728ad53f8f4f445b9279149e9",
545
+ "language": "Python",
546
+ "lines": 95,
547
+ "truncated": false,
548
+ "block": 3,
549
+ "row": 21652
550
+ },
551
+ {
552
+ "path": "fissa/fissa/neuropil.py",
553
+ "sha256": "7693095e968f6b5bf0b96e03f0e912f6d7856d32223cae349e212bff30eef51e",
554
+ "language": "Python",
555
+ "lines": 237,
556
+ "truncated": false,
557
+ "block": 3,
558
+ "row": 24777
559
+ },
560
+ {
561
+ "path": "fissa/fissa/readimagejrois.py",
562
+ "sha256": "0b417d11b351462482cdeef8cd9866a96d41e168d681af7b2efaaa9157bb1f8d",
563
+ "language": "Python",
564
+ "lines": 436,
565
+ "truncated": false,
566
+ "block": 3,
567
+ "row": 26341
568
+ },
569
+ {
570
+ "path": "fissa/fissa/roitools.py",
571
+ "sha256": "ffe83794864b28cd9e216e76d74dc743468e242d46ee536d419910d9e7b9b714",
572
+ "language": "Python",
573
+ "lines": 436,
574
+ "truncated": false,
575
+ "block": 3,
576
+ "row": 26074
577
+ },
578
+ {
579
+ "path": "fissa/fissa/tests/base_test.py",
580
+ "sha256": "30bb75353547a990c14de27d470643205d730e585771fdaf87f271702b214363",
581
+ "language": "Python",
582
+ "lines": 74,
583
+ "truncated": false,
584
+ "block": 3,
585
+ "row": 20747
586
+ },
587
+ {
588
+ "path": "fissa/fissa/tests/generate_downsampled_resources.py",
589
+ "sha256": "649d104a982b0e8f3470c2309a8ca58f1233544538bba24ce8c9cc329e921fb5",
590
+ "language": "Python",
591
+ "lines": 390,
592
+ "truncated": false,
593
+ "block": 3,
594
+ "row": 26172
595
+ },
596
+ {
597
+ "path": "fissa/fissa/tests/test_ROI.py",
598
+ "sha256": "a2f8af8f5184e11a9addcc1c133671d41ea6a24f5adc0e1ed40ee0996eea4d62",
599
+ "language": "Python",
600
+ "lines": 45,
601
+ "truncated": false,
602
+ "block": 3,
603
+ "row": 19687
604
+ },
605
+ {
606
+ "path": "fissa/fissa/tests/test_core.py",
607
+ "sha256": "4014cb69170b366049e7a390e080ec1afcb14907d98f3ef819be651a8fd22577",
608
+ "language": "Python",
609
+ "lines": 363,
610
+ "truncated": false,
611
+ "block": 3,
612
+ "row": 26571
613
+ },
614
+ {
615
+ "path": "fissa/fissa/tests/test_datahandler.py",
616
+ "sha256": "db72aad606c823fecd8623016dbed56c1071c6101c227facd82460b727155f27",
617
+ "language": "Python",
618
+ "lines": 94,
619
+ "truncated": false,
620
+ "block": 3,
621
+ "row": 21138
622
+ },
623
+ {
624
+ "path": "fissa/fissa/tests/test_datahandler_framebyframe.py",
625
+ "sha256": "c542f1401aa7025e160da3901f916b94c84f9d2ffaa403c59e652d273875b7e0",
626
+ "language": "Python",
627
+ "lines": 90,
628
+ "truncated": false,
629
+ "block": 3,
630
+ "row": 21133
631
+ },
632
+ {
633
+ "path": "fissa/fissa/tests/test_deltaf.py",
634
+ "sha256": "dea8f8f302a19c59577621237caebb8fa05f4172ba42ff26b4dd688b025b999a",
635
+ "language": "Python",
636
+ "lines": 105,
637
+ "truncated": false,
638
+ "block": 3,
639
+ "row": 21680
640
+ },
641
+ {
642
+ "path": "fissa/fissa/tests/test_neuropil.py",
643
+ "sha256": "420d8ff6ae50aa4f6f569baaf8d8d164766879e2e867793e3bd8a6df1dc7f92c",
644
+ "language": "Python",
645
+ "lines": 69,
646
+ "truncated": false,
647
+ "block": 3,
648
+ "row": 20827
649
+ },
650
+ {
651
+ "path": "fissa/fissa/tests/test_readimagejrois.py",
652
+ "sha256": "be8124814e574d5df28a217f4576534256edec40ead14e86bd6e1fe01eaa42b4",
653
+ "language": "Python",
654
+ "lines": 200,
655
+ "truncated": false,
656
+ "block": 3,
657
+ "row": 23663
658
+ },
659
+ {
660
+ "path": "fissa/fissa/tests/test_roitools.py",
661
+ "sha256": "3d302baeb5348b7dfdd5e0537c46acbccfc6a28aebf2a1498a7431b906c402d4",
662
+ "language": "Python",
663
+ "lines": 320,
664
+ "truncated": false,
665
+ "block": 3,
666
+ "row": 25379
667
+ },
668
+ {
669
+ "path": "fissa/setup.py",
670
+ "sha256": "4d86e1dc12f2a15edb89205e2cd6f23a496d0c8881379bdd077e283df5d40983",
671
+ "language": "Python",
672
+ "lines": 89,
673
+ "truncated": false,
674
+ "block": 3,
675
+ "row": 21175
676
+ },
677
+ {
678
+ "path": "helperFcns/BFmap/BFuDBcalc.m",
679
+ "sha256": "b7fb454809a6738f939596ddc51be129cf3c49917fa12a859956834a7c2c67f0",
680
+ "language": "MATLAB",
681
+ "lines": 11,
682
+ "truncated": false,
683
+ "block": 3,
684
+ "row": 8997
685
+ },
686
+ {
687
+ "path": "helperFcns/BFmap/TRFmap.m",
688
+ "sha256": "1be76696947915575d21ab61853ed1a347451505c17c10df3e58aaf1feff54b1",
689
+ "language": "MATLAB",
690
+ "lines": 217,
691
+ "truncated": false,
692
+ "block": 3,
693
+ "row": 16009
694
+ },
695
+ {
696
+ "path": "helperFcns/BFmap/compileTRF.m",
697
+ "sha256": "4b2e862c26e0104e61831c026d8934396cfbd0490ede6052e76ffd13a53941c0",
698
+ "language": "MATLAB",
699
+ "lines": 180,
700
+ "truncated": false,
701
+ "block": 3,
702
+ "row": 15670
703
+ },
704
+ {
705
+ "path": "helperFcns/BFmap/extractMapPulseParams.m",
706
+ "sha256": "c152a517f81bf3167616badb65d54fc28e2905bb3871d73eca4dafb19eadef08",
707
+ "language": "MATLAB",
708
+ "lines": 19,
709
+ "truncated": false,
710
+ "block": 3,
711
+ "row": 10402
712
+ },
713
+ {
714
+ "path": "helperFcns/BFmap/getMapAnalysisParams.m",
715
+ "sha256": "7042077d3cc6b1bf808b416de8004201d7be84c06ce1f0339284fd0b8d8e30e2",
716
+ "language": "MATLAB",
717
+ "lines": 72,
718
+ "truncated": false,
719
+ "block": 3,
720
+ "row": 13004
721
+ },
722
+ {
723
+ "path": "helperFcns/BFmap/monotonicityCalc.m",
724
+ "sha256": "dfa420ae81281b4f2b0dedcdc5a6051fa67c43719737191cc3210c5b0ffd1c41",
725
+ "language": "MATLAB",
726
+ "lines": 63,
727
+ "truncated": false,
728
+ "block": 3,
729
+ "row": 12379
730
+ },
731
+ {
732
+ "path": "helperFcns/BFmap/plotTRFmap.m",
733
+ "sha256": "4d1ee2bba1a0b5ea1575591a9fe8275e81fa014b625343389c43bf3ad0492378",
734
+ "language": "MATLAB",
735
+ "lines": 205,
736
+ "truncated": false,
737
+ "block": 3,
738
+ "row": 15959
739
+ },
740
+ {
741
+ "path": "helperFcns/BFmap/repFreqMask2linTRFidx.m",
742
+ "sha256": "eb7749e2ac86b1bd3e237a4b2639e86896ebe797da7fa4fdc5cfd90f22ce669f",
743
+ "language": "MATLAB",
744
+ "lines": 17,
745
+ "truncated": false,
746
+ "block": 3,
747
+ "row": 9511
748
+ },
749
+ {
750
+ "path": "helperFcns/BFmap/tuningQualityToTtrfAnml.m",
751
+ "sha256": "b3b083f4d8e5a3d9ea9769a2c6dc8e4f54cb2c02ad072db71303f293a76f409d",
752
+ "language": "MATLAB",
753
+ "lines": 46,
754
+ "truncated": false,
755
+ "block": 3,
756
+ "row": 11498
757
+ },
758
+ {
759
+ "path": "helperFcns/cellFRA2dPrime.m",
760
+ "sha256": "6a1b7a7c5a7fff4b0e4763cc3f49db3b8bc35cfbab253ae984e3d2d106e83c1e",
761
+ "language": "MATLAB",
762
+ "lines": 42,
763
+ "truncated": false,
764
+ "block": 3,
765
+ "row": 10597
766
+ },
767
+ {
768
+ "path": "helperFcns/dFF/baseIDXfromPTonset.m",
769
+ "sha256": "483758298f4e7c010905e421c13c14570e5fdce6136cdb731f9df38f790aa019",
770
+ "language": "MATLAB",
771
+ "lines": 23,
772
+ "truncated": false,
773
+ "block": 3,
774
+ "row": 9621
775
+ },
776
+ {
777
+ "path": "helperFcns/dFF/dFcalc.m",
778
+ "sha256": "ab2454f1eaef9fb6d060a860775b0dffd06826ac5e938fadb6c42b1a519ed10b",
779
+ "language": "MATLAB",
780
+ "lines": 23,
781
+ "truncated": false,
782
+ "block": 3,
783
+ "row": 9306
784
+ },
785
+ {
786
+ "path": "helperFcns/dFF/dFoFcalc.m",
787
+ "sha256": "85f59126fb6e7d00968a64633c4fa693e980e0ea400c7181a9c793071243f803",
788
+ "language": "MATLAB",
789
+ "lines": 39,
790
+ "truncated": false,
791
+ "block": 3,
792
+ "row": 10910
793
+ },
794
+ {
795
+ "path": "helperFcns/dFF/pkFcalc.m",
796
+ "sha256": "301aab34034f8feb0db78fbf508ad21e829a95cd1b6f73e5ae43ac0cb581a964",
797
+ "language": "MATLAB",
798
+ "lines": 47,
799
+ "truncated": false,
800
+ "block": 3,
801
+ "row": 12362
802
+ },
803
+ {
804
+ "path": "helperFcns/dataOrg/FISSAoutput2tifFileList.m",
805
+ "sha256": "d3368a3b600d6579e15324f8840ca01a51edac12b331edb0a0078cdd730fe2f8",
806
+ "language": "MATLAB",
807
+ "lines": 22,
808
+ "truncated": false,
809
+ "block": 3,
810
+ "row": 10222
811
+ },
812
+ {
813
+ "path": "helperFcns/dataOrg/anmlROIbyStimTable.m",
814
+ "sha256": "eaef667c27cfacc732aa6ba9222e3c9c06f104bb069bab44cc301d0162258b0f",
815
+ "language": "MATLAB",
816
+ "lines": 118,
817
+ "truncated": false,
818
+ "block": 3,
819
+ "row": 14444
820
+ },
821
+ {
822
+ "path": "helperFcns/dataOrg/compileAnimalDataTable.m",
823
+ "sha256": "40bac4703102fa14e9dea3d437bde918df3dbe6c922c34c096980fb1e9dca8a0",
824
+ "language": "MATLAB",
825
+ "lines": 249,
826
+ "truncated": false,
827
+ "block": 3,
828
+ "row": 16190
829
+ },
830
+ {
831
+ "path": "helperFcns/dataOrg/extractStimParams.m",
832
+ "sha256": "b5dbf0bfcc9fd2ba77a35c23cf8458502470b59032f10896e287d99b8a514349",
833
+ "language": "MATLAB",
834
+ "lines": 54,
835
+ "truncated": false,
836
+ "block": 3,
837
+ "row": 12357
838
+ },
839
+ {
840
+ "path": "helperFcns/dataOrg/getAnalysisParams.m",
841
+ "sha256": "ebecb3c58be16f7586271be03d50a4b0d7b8e21406bdb5ec1217dc9f896fb30c",
842
+ "language": "MATLAB",
843
+ "lines": 81,
844
+ "truncated": false,
845
+ "block": 3,
846
+ "row": 13671
847
+ },
848
+ {
849
+ "path": "helperFcns/dataOrg/getContrastDRCvars.m",
850
+ "sha256": "9d7294aeadb7d81a03c8e3d39d40a99dfa8aa9490b9f706c3846324d0e0f2c26",
851
+ "language": "MATLAB",
852
+ "lines": 17,
853
+ "truncated": false,
854
+ "block": 3,
855
+ "row": 9489
856
+ },
857
+ {
858
+ "path": "helperFcns/dataOrg/moCorRawF2tifList.m",
859
+ "sha256": "0bd76ac5bc0024b8b3535eb35529b4745578e0d8d94a1338eb7b1f91394085f6",
860
+ "language": "MATLAB",
861
+ "lines": 58,
862
+ "truncated": false,
863
+ "block": 3,
864
+ "row": 12181
865
+ },
866
+ {
867
+ "path": "helperFcns/dataOrg/oneAnimalPkPTresp.m",
868
+ "sha256": "ebe3a44dbc6e237a5c6aad84c4cb82de7665f37423d9f0aaca13c0505f4af21b",
869
+ "language": "MATLAB",
870
+ "lines": 186,
871
+ "truncated": false,
872
+ "block": 3,
873
+ "row": 15921
874
+ },
875
+ {
876
+ "path": "helperFcns/dataOrg/stimParams2TifTable.m",
877
+ "sha256": "46624a825c76238744c233c6d82a232260d39b12620c9a68c8b898ba9f3c15af",
878
+ "language": "MATLAB",
879
+ "lines": 11,
880
+ "truncated": false,
881
+ "block": 3,
882
+ "row": 9173
883
+ },
884
+ {
885
+ "path": "helperFcns/dataOrg/updateTifFileList.m",
886
+ "sha256": "dbb0710efd8a5f18fef1dbe8a39b1c0f5cf43c8ec1303891a911c71f1175dd7c",
887
+ "language": "MATLAB",
888
+ "lines": 37,
889
+ "truncated": false,
890
+ "block": 3,
891
+ "row": 11643
892
+ },
893
+ {
894
+ "path": "helperFcns/general/scaleZeroToOne.m",
895
+ "sha256": "07a2c9d54add55e747a427bdc473ea52a7438709f98798a458d9f2a230e5a354",
896
+ "language": "MATLAB",
897
+ "lines": 6,
898
+ "truncated": false,
899
+ "block": 3,
900
+ "row": 8257
901
+ },
902
+ {
903
+ "path": "helperFcns/plotting/xlabelLowHighPkRespRatio.m",
904
+ "sha256": "8d7e67d69a4caf7788761004289c896a0d5d0fdb018cd2415ca66206d5d81b95",
905
+ "language": "MATLAB",
906
+ "lines": 24,
907
+ "truncated": false,
908
+ "block": 3,
909
+ "row": 9855
910
+ },
911
+ {
912
+ "path": "helperFcns/plotting/ylabelLowHighPkRespRatio.m",
913
+ "sha256": "25d91112869e50342eac4d7944550e867b460188da460e56b9a4fabe84862bbc",
914
+ "language": "MATLAB",
915
+ "lines": 45,
916
+ "truncated": false,
917
+ "block": 3,
918
+ "row": 11344
919
+ },
920
+ {
921
+ "path": "helperFcns/roi/TifROImask2rawFroi.m",
922
+ "sha256": "b03ea62b6d51bd815f25d047c6a921fb0504e6e5d37c2b06b0e62b512216b71c",
923
+ "language": "MATLAB",
924
+ "lines": 26,
925
+ "truncated": false,
926
+ "block": 3,
927
+ "row": 9430
928
+ },
929
+ {
930
+ "path": "helperFcns/roi/intersectROIfiles.m",
931
+ "sha256": "70fc28e5288f1a510c931e89d2903af490d61edac381e8f2d6b5b79b91f012f3",
932
+ "language": "MATLAB",
933
+ "lines": 27,
934
+ "truncated": false,
935
+ "block": 3,
936
+ "row": 10734
937
+ },
938
+ {
939
+ "path": "helperFcns/roi/mask2polyCoord.m",
940
+ "sha256": "e7e2a848a54252076d4bd8f0d675be425ab77ae8ba152628dd3ce5c8d88909ca",
941
+ "language": "MATLAB",
942
+ "lines": 37,
943
+ "truncated": false,
944
+ "block": 3,
945
+ "row": 9776
946
+ },
947
+ {
948
+ "path": "helperFcns/roi/orderEllipsePtOnCurve.m",
949
+ "sha256": "71710d5d3ad04c0286b3db33a5e48f095c0c9f59525eb8fed0f59fc9590b30cb",
950
+ "language": "MATLAB",
951
+ "lines": 20,
952
+ "truncated": false,
953
+ "block": 3,
954
+ "row": 9725
955
+ },
956
+ {
957
+ "path": "helperFcns/tif/justLoadTif.m",
958
+ "sha256": "dd4cbc126828682a5c10e0a2d4a68ef4a5aed6f8dbe013f8e51fa7aad0c1bc42",
959
+ "language": "MATLAB",
960
+ "lines": 18,
961
+ "truncated": false,
962
+ "block": 3,
963
+ "row": 9338
964
+ },
965
+ {
966
+ "path": "helperFcns/tif/readSCIMtif.m",
967
+ "sha256": "6519ed985b9f80c9d1213bea81c10c6471b499802b317783795e691b8fd57862",
968
+ "language": "MATLAB",
969
+ "lines": 154,
970
+ "truncated": false,
971
+ "block": 3,
972
+ "row": 15134
973
+ },
974
+ {
975
+ "path": "helperFcns/tif/redGreenMerge.m",
976
+ "sha256": "0f22c272bc3e5b7441a2efef53d98aa8fc67c39fa0bd93f5eb78c003a423efbb",
977
+ "language": "MATLAB",
978
+ "lines": 5,
979
+ "truncated": false,
980
+ "block": 3,
981
+ "row": 8374
982
+ },
983
+ {
984
+ "path": "helperFcns/tif/splitTifChans.m",
985
+ "sha256": "4fb8a364833cecfeea7fe15c5b2729346eaae8e94942bad5ed192c6300d201cf",
986
+ "language": "MATLAB",
987
+ "lines": 60,
988
+ "truncated": false,
989
+ "block": 3,
990
+ "row": 12370
991
+ },
992
+ {
993
+ "path": "helperFcns/tif/writeMoCorTifs.m",
994
+ "sha256": "adf6f392a9f956f8e6d66e8cba0c0d3103b7cb6351e7e76a2240e6f7820dd1d8",
995
+ "language": "MATLAB",
996
+ "lines": 46,
997
+ "truncated": false,
998
+ "block": 3,
999
+ "row": 11563
1000
+ }
1001
+ ]
1002
+ }
manifests/f6/figshare__29941784.json ADDED
@@ -0,0 +1,84 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "figshare:29941784",
4
+ "url": "10.6084/m9.figshare.29941784",
5
+ "host": "figshare.com",
6
+ "commit": "",
7
+ "license": "CC-BY-4.0",
8
+ "license_confirmed_by": "license of the archive's record",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "Example_Codes.py",
13
+ "sha256": "3bf221e8c092e6602c88adec4d4417d38b797bcca1f2d62c08fdefa514a941d5",
14
+ "language": "Python",
15
+ "lines": 237,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 26018
19
+ },
20
+ {
21
+ "path": "ReadMe.txt",
22
+ "sha256": "5d40f1c5a637dfa2c244a804b5968c20d9a00affa368f8095ff594cac7378b70",
23
+ "language": "Text",
24
+ "lines": 86,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2513
28
+ },
29
+ {
30
+ "path": "chebyshev.jl",
31
+ "sha256": "8ddf4d9065a1d53e3a6a267394afc43bed2f09b23d8ffcf2f5c09a51ed55ed75",
32
+ "language": "Julia",
33
+ "lines": 9,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 6984
37
+ },
38
+ {
39
+ "path": "coefficients_fitting.jl",
40
+ "sha256": "5af989a545e19cf16706e828d03e9930751e34d2376b4c557e68f1915762b777",
41
+ "language": "Julia",
42
+ "lines": 904,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 7030
46
+ },
47
+ {
48
+ "path": "plotting.jl",
49
+ "sha256": "bd408079191a4e751425b6a2f40c86fb8d22ef9de9a57493d39901700cccc73a",
50
+ "language": "Julia",
51
+ "lines": 34,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 7003
55
+ },
56
+ {
57
+ "path": "utils.jl",
58
+ "sha256": "a7ef259ff16bc4356c0fb47cf273952edbf9c11c0389576c770f1593ab5c08e5",
59
+ "language": "Julia",
60
+ "lines": 239,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 7016
64
+ },
65
+ {
66
+ "path": "wavelet.jl",
67
+ "sha256": "9633af65a18820e5b203c94972fe2773384c543b8f9817ed6f7415fcc7fbecb5",
68
+ "language": "Julia",
69
+ "lines": 190,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 7017
73
+ },
74
+ {
75
+ "path": "wavelet_analysis.jl",
76
+ "sha256": "ab6396000c66bff5b77693bb9642257c1ac851c362f0bcfef3862716534a4b29",
77
+ "language": "Julia",
78
+ "lines": 438,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 7027
82
+ }
83
+ ]
84
+ }
manifests/f6/github.com__fraunhoferchalmerscentre__neuralodepopulation.json ADDED
@@ -0,0 +1,111 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/fraunhoferchalmerscentre/neuralodepopulation",
4
+ "url": "https://github.com/FraunhoferChalmersCentre/neuralODEpopulation",
5
+ "host": "github.com",
6
+ "commit": "ff72acad955bc8fa489d161f8e46fdfae1b71547",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "4ac7c426458bcaed8a56b399d47ef2fbe3533367a4f4fcddef7c7f843f076c7a",
14
+ "language": "License",
15
+ "lines": 21,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8056
19
+ },
20
+ {
21
+ "path": "lib/models/NNmodels.py",
22
+ "sha256": "d3ed69cfbdcbcb7b9ff04d66c967ab9a9ca4bd09098282c694ab710258a129e5",
23
+ "language": "Python",
24
+ "lines": 751,
25
+ "truncated": false,
26
+ "block": 3,
27
+ "row": 27442
28
+ },
29
+ {
30
+ "path": "lib/utils/utils_data_generation.py",
31
+ "sha256": "7ae80ad381420617e347061ad9e8f8d5b13544a18512b13cbbc62f21bb14a6b6",
32
+ "language": "Python",
33
+ "lines": 1173,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 27790
37
+ },
38
+ {
39
+ "path": "lib/utils/utils_post_processing.py",
40
+ "sha256": "b338b0c165e96c0d923e61d09bdaf90ed560c0e97018fca2f98b5dc1c1e36982",
41
+ "language": "Python",
42
+ "lines": 1886,
43
+ "truncated": false,
44
+ "block": 4,
45
+ "row": 45
46
+ },
47
+ {
48
+ "path": "lib/utils/utils_preprocess.py",
49
+ "sha256": "703bdec3e10c95d14970dd55325554ff8ab0fa44913501f794d14da10f09cc9e",
50
+ "language": "Python",
51
+ "lines": 925,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 27615
55
+ },
56
+ {
57
+ "path": "lib/utils/utils_shared.py",
58
+ "sha256": "3f35ce9649126adc912815799fe19a9c17bcc6fb975e8f9e77d3ec4b5a90c0b6",
59
+ "language": "Python",
60
+ "lines": 527,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 26819
64
+ },
65
+ {
66
+ "path": "lib/utils/utils_training.py",
67
+ "sha256": "13feee13569be28c5ec18ec6edf2361edc4fcaeb0a9369dac931ce267ebdfa3c",
68
+ "language": "Python",
69
+ "lines": 828,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 27441
73
+ },
74
+ {
75
+ "path": "readme.md",
76
+ "sha256": "6fae5a4eec2f6f16064df298155c466f6a101c0a2520198ebdc6d51a57669821",
77
+ "language": "Text",
78
+ "lines": 7,
79
+ "truncated": false,
80
+ "block": 4,
81
+ "row": 2406
82
+ },
83
+ {
84
+ "path": "scripts/generate_data.py",
85
+ "sha256": "c58de32d063071eaccfb5d7ebeb65e9d2ae7ed3ee40c9c3377650c5293cab774",
86
+ "language": "Python",
87
+ "lines": 574,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 26980
91
+ },
92
+ {
93
+ "path": "scripts/main_clinical_data.py",
94
+ "sha256": "b2162315b45ea3890863c24aace91bc278aaef9686e02be92051881a5a829830",
95
+ "language": "Python",
96
+ "lines": 311,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 24983
100
+ },
101
+ {
102
+ "path": "scripts/main_simulated_data.py",
103
+ "sha256": "13b810e5cdf246cb4a8ab7b47baa7699f21c344993e7e3c321c479d38bf7b85b",
104
+ "language": "Python",
105
+ "lines": 423,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 25655
109
+ }
110
+ ]
111
+ }
manifests/f6/github.com__oranges7__vcboost.json ADDED
@@ -0,0 +1,165 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/oranges7/vcboost",
4
+ "url": "https://github.com/oranges7/VCboost",
5
+ "host": "github.com",
6
+ "commit": "1be2522c18e10d5fc4f39a5ad727c4caf1247873",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "8bbba5d395f437043098f338ee0f3b30acff3e25a85cbc59948a2a06a1c480c1",
14
+ "language": "License",
15
+ "lines": 21,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 7937
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "24fac93ad4403a60c0e3ab1e98a9e9d0aa9a74142d7f46da2019b9f00e80b95e",
23
+ "language": "Text",
24
+ "lines": 122,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2488
28
+ },
29
+ {
30
+ "path": "script/predict/batch_con.py",
31
+ "sha256": "12915d212052df2f5acf54e779e0338d7053a42445e29f8e8bb759224ae61b83",
32
+ "language": "Python",
33
+ "lines": 91,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 21618
37
+ },
38
+ {
39
+ "path": "script/predict/generate_chr.py",
40
+ "sha256": "8930310841ab7285d52ef2db59ef4be955ad74b96ad9b391c8d371da789edce5",
41
+ "language": "Python",
42
+ "lines": 14,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 18669
46
+ },
47
+ {
48
+ "path": "script/predict/generate_hap_both_onehot_refalt.py",
49
+ "sha256": "4cadce9843f54427c3a5de1cc1ea55ff4233868af45441b2d1376e91a364e539",
50
+ "language": "Python",
51
+ "lines": 262,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 25453
55
+ },
56
+ {
57
+ "path": "script/predict/pred_batch.py",
58
+ "sha256": "362e1f6c45f70665e7479e3e98634b0e77b768e45159f2fa44a4c11742f09e68",
59
+ "language": "Python",
60
+ "lines": 298,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 25228
64
+ },
65
+ {
66
+ "path": "script/predict/run_predict.sh",
67
+ "sha256": "0f539c1b8cb208d32d3b29d9ccb0d93b26b40841632ff75f7c8c1770f13079fe",
68
+ "language": "Shell",
69
+ "lines": 148,
70
+ "truncated": false,
71
+ "block": 4,
72
+ "row": 2163
73
+ },
74
+ {
75
+ "path": "script/predict/select_snp_for_phase.py",
76
+ "sha256": "a7f434989dba76f926660e99c3c6e321cec11b5351cafb1213c905b4d7bfac01",
77
+ "language": "Python",
78
+ "lines": 76,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 20781
82
+ },
83
+ {
84
+ "path": "script/predict/split_chr.py",
85
+ "sha256": "0ac5e293c870fccd42e2f77dd5ee99f3fcb94d4e3a8d2b14e90a760572feb9f3",
86
+ "language": "Python",
87
+ "lines": 50,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 20167
91
+ },
92
+ {
93
+ "path": "script/train/generate_hap_both_onehot_refalt.py",
94
+ "sha256": "79536d5d34c54f45fc2c220627a43bc73c64cee7e4ed89d761c9f849c15768a9",
95
+ "language": "Python",
96
+ "lines": 270,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 25613
100
+ },
101
+ {
102
+ "path": "script/train/model_train.py",
103
+ "sha256": "a664e2c14316010954e1fc3eac2c6c8b2836c62cf706185f6d3b52a00f826c12",
104
+ "language": "Python",
105
+ "lines": 323,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 25460
109
+ },
110
+ {
111
+ "path": "script/train/run_train.sh",
112
+ "sha256": "22c8b31e5b9742cf36d450e63adb64a8af4c40f6bde2b30420ecef5305204f40",
113
+ "language": "Shell",
114
+ "lines": 223,
115
+ "truncated": false,
116
+ "block": 4,
117
+ "row": 2225
118
+ },
119
+ {
120
+ "path": "script/train/select_pf_indel.py",
121
+ "sha256": "59b5ea62f5e6413a13ea083ec433137cf92e7f7bf5eb0838903ff093a4d4cdea",
122
+ "language": "Python",
123
+ "lines": 47,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 19472
127
+ },
128
+ {
129
+ "path": "script/train/select_pf_snp.py",
130
+ "sha256": "18909825fb0a58c21bc118286c14ccd3ea3f48d3e87c356212eda7a60774a342",
131
+ "language": "Python",
132
+ "lines": 45,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 19507
136
+ },
137
+ {
138
+ "path": "script/train/select_snp_for_phase.py",
139
+ "sha256": "b87a59171e26120ccb17fb194c38c654cf91246bb4634e02c936c4483eb96f95",
140
+ "language": "Python",
141
+ "lines": 74,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 20790
145
+ },
146
+ {
147
+ "path": "script/train/split_chr.py",
148
+ "sha256": "45432d349d8aa471a7a8ff137fc3ecdb8e2c7b987a3c36bfebe6a0f5a5c33889",
149
+ "language": "Python",
150
+ "lines": 31,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 19032
154
+ },
155
+ {
156
+ "path": "vcboost.sh",
157
+ "sha256": "ce7c480170bc9e47c06aa00714aadeebac12b330616115028a979bf7702112ac",
158
+ "language": "Shell",
159
+ "lines": 8,
160
+ "truncated": false,
161
+ "block": 4,
162
+ "row": 1387
163
+ }
164
+ ]
165
+ }
manifests/f7/github.com__a96123155__utr-lm.json ADDED
@@ -0,0 +1,102 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/a96123155/utr-lm",
4
+ "url": "https://github.com/a96123155/UTR-LM",
5
+ "host": "github.com",
6
+ "commit": "b77b589bf182eb9de6a1a5024fa09d44294d94fc",
7
+ "license": "GPL-3.0",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986",
14
+ "language": "License",
15
+ "lines": 674,
16
+ "truncated": false,
17
+ "block": 1,
18
+ "row": 2235
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "879fe53304a4df8d02250e543cc1a1a9571021bef65df2e8526ae446e07c45ac",
23
+ "language": "Text",
24
+ "lines": 130,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2611
28
+ },
29
+ {
30
+ "path": "Scripts/In-Housing/6_unFinetune_results.ipynb",
31
+ "sha256": "5c5ac8bf65b2a416924573d91e75c93e615561cf265a2559f2610233cca914f3",
32
+ "language": "Jupyter",
33
+ "lines": 292,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 7626
37
+ },
38
+ {
39
+ "path": "Scripts/In-Housing/7_Optimus_retrained.ipynb",
40
+ "sha256": "149d773ab3a3c38f8f8fcbabd66153f234a2339a4d768e16748a1f78d81a7157",
41
+ "language": "Jupyter",
42
+ "lines": 221,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 7524
46
+ },
47
+ {
48
+ "path": "Scripts/In-Housing/8_finetune_results.ipynb",
49
+ "sha256": "806bbeb1c5aa7465cf493bdadb35754d4a57664389e39e493b9db932ee51cc80",
50
+ "language": "Jupyter",
51
+ "lines": 299,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 7597
55
+ },
56
+ {
57
+ "path": "Scripts/In-Housing/Hypothesis_PairedTtest.ipynb",
58
+ "sha256": "7fd480c620e6c5bfb1b190f1ba29ab25fe49440d63d1aa8bbdcea3a2c126d59c",
59
+ "language": "Jupyter",
60
+ "lines": 85,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 7201
64
+ },
65
+ {
66
+ "path": "Scripts/Results/AttentionBased_Interpretation/IndependentHuman_PushLen50_ConvolutionalOperation_Attention_KmerMotifs.ipynb",
67
+ "sha256": "922157f17943b6405a7e7a428a5c3dd6c37b6db58970688b4053045864ee1eb0",
68
+ "language": "Jupyter",
69
+ "lines": 572,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 7742
73
+ },
74
+ {
75
+ "path": "Scripts/Results/AttentionBased_Interpretation/MJ_Interpretability_IndependentHuman_LowHighMRLs_ATG_CCACC.ipynb",
76
+ "sha256": "4ae237e21fab05c1e447f43e16b876cacf5403f192a611b2973a6b00f5c9ebe2",
77
+ "language": "Jupyter",
78
+ "lines": 663,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 7787
82
+ },
83
+ {
84
+ "path": "Scripts/Results/AttentionBased_Interpretation/U1_ConvolutionalOperation_Attention_KmerMotifs.ipynb",
85
+ "sha256": "a4e8c06dddcef99ea7822854ff6bb730337e25bebaf2e0d35158f2941250fc73",
86
+ "language": "Jupyter",
87
+ "lines": 501,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 7705
91
+ },
92
+ {
93
+ "path": "Scripts/Results/AttentionBased_Interpretation/fivespecies_representation-PCA-KNN-UMAP.ipynb",
94
+ "sha256": "17312ff694fb4bc3e57f5a1d738aeb20e61c675c1590d9a70ae6a708dd2a935d",
95
+ "language": "Jupyter",
96
+ "lines": 742,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 7792
100
+ }
101
+ ]
102
+ }
manifests/f7/github.com__iamnielsjanssen__display_melodics.json ADDED
@@ -0,0 +1,39 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/iamnielsjanssen/display_melodics",
4
+ "url": "https://github.com/iamnielsjanssen/display_melodics",
5
+ "host": "github.com",
6
+ "commit": "a349c4a940c4757585d83d631a35199c902b0a9f",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "459bfa24a703fadc51dc76198b97f74ae8c29031923b8315f9d70f77183708da",
14
+ "language": "License",
15
+ "lines": 22,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8055
19
+ },
20
+ {
21
+ "path": "README",
22
+ "sha256": "2218fdd82b20e587a8963a9eba5c77a86d1960d3485279ae59646b2d822ed062",
23
+ "language": "Text",
24
+ "lines": 28,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2348
28
+ },
29
+ {
30
+ "path": "display_melodics.py",
31
+ "sha256": "8aee9500118c7e04fe4909d2dc78a3d6e0ceba9dfb1624bb29fa28bfad77edf1",
32
+ "language": "Python",
33
+ "lines": 124,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 21967
37
+ }
38
+ ]
39
+ }
manifests/f7/github.com__kpm-floesch__nicetfrplot.json ADDED
@@ -0,0 +1,39 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/kpm-floesch/nicetfrplot",
4
+ "url": "https://github.com/kpm-floesch/niceTFRplot",
5
+ "host": "github.com",
6
+ "commit": "db346ac6049047709a01960d5bc9db40db4d7c0e",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "47a88e99b37eb9c6458f05e49018754b344c63a1912c9a0f884cb8c4fcf290f0",
14
+ "language": "License",
15
+ "lines": 21,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8047
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "ae3b6cf6142ba0ecebe30ed587fcf911e4cec30a51b4f170c4a992d55fb8327a",
23
+ "language": "Text",
24
+ "lines": 18,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2381
28
+ },
29
+ {
30
+ "path": "niceTFRplot.m",
31
+ "sha256": "f70d3aa4bd226fa751fe9b4c4ebfcff29011e329878994f14343a448dd797e1e",
32
+ "language": "MATLAB",
33
+ "lines": 249,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 16198
37
+ }
38
+ ]
39
+ }
manifests/f7/github.com__oxpig__calm.json ADDED
@@ -0,0 +1,165 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/oxpig/calm",
4
+ "url": "https://github.com/oxpig/CaLM",
5
+ "host": "github.com",
6
+ "commit": "24187ea44744ca548b747ad262058f3463589f8e",
7
+ "license": "BSD-3-Clause",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "CaLM.ipynb",
13
+ "sha256": "cdc23473615dea07d3b2b66656338e2732f2e77509627d132d21e89adf3c05e3",
14
+ "language": "Jupyter",
15
+ "lines": 124,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 7266
19
+ },
20
+ {
21
+ "path": "LICENSE",
22
+ "sha256": "c504ab83686ed8e077f669caae2aeb107a4dfb152767a3647ab0110d06b0f763",
23
+ "language": "License",
24
+ "lines": 29,
25
+ "truncated": false,
26
+ "block": 3,
27
+ "row": 8120
28
+ },
29
+ {
30
+ "path": "README.md",
31
+ "sha256": "45fe958d17d3d2f650a391c70dd3d607e42edfa972408d9227bac99a345cb624",
32
+ "language": "Text",
33
+ "lines": 30,
34
+ "truncated": false,
35
+ "block": 4,
36
+ "row": 2327
37
+ },
38
+ {
39
+ "path": "calm/__init__.py",
40
+ "sha256": "e5b552bb7c44462af4ac1da5883e0fab6c2762901cc55912dfb4f1f8ee961164",
41
+ "language": "Python",
42
+ "lines": 1,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 17373
46
+ },
47
+ {
48
+ "path": "calm/alphabet.py",
49
+ "sha256": "16e0745a5c3dd6fa0a2fbca0bf8e0e74fc07ee01e66c293f97214c33f1bae895",
50
+ "language": "Python",
51
+ "lines": 208,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 24423
55
+ },
56
+ {
57
+ "path": "calm/dataset.py",
58
+ "sha256": "aabcd42911438d06b19db1115b3f4ddc91c3c3d054dfc6ce170f362a26365aa5",
59
+ "language": "Python",
60
+ "lines": 34,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 18889
64
+ },
65
+ {
66
+ "path": "calm/model.py",
67
+ "sha256": "f0d2ad4da037f39a554f37fd0455df382158119222f61fa99a534c7d1014e6a0",
68
+ "language": "Python",
69
+ "lines": 178,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 23760
73
+ },
74
+ {
75
+ "path": "calm/modules.py",
76
+ "sha256": "8e1fad1ddde3a1025bc59a7066c65ba10a0ea372fb3493915d9c129847c7c2f5",
77
+ "language": "Python",
78
+ "lines": 282,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 25260
82
+ },
83
+ {
84
+ "path": "calm/multihead_attention.py",
85
+ "sha256": "c9c1ebf2b0dd2a9c901395cdb8f1fac038b54a4dd18453869b15141436c99f85",
86
+ "language": "Python",
87
+ "lines": 511,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 27067
91
+ },
92
+ {
93
+ "path": "calm/pipeline.py",
94
+ "sha256": "02c70e66cb7ae9276ff456dceb9a502637b4ebbdfd0dbcf6cb407e418c1f9182",
95
+ "language": "Python",
96
+ "lines": 276,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 25167
100
+ },
101
+ {
102
+ "path": "calm/pretrained.py",
103
+ "sha256": "d3d9c5dc1ece4a408b33f343e77ba173f215dba7d2f53f84f6f92009351544e3",
104
+ "language": "Python",
105
+ "lines": 96,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 21612
109
+ },
110
+ {
111
+ "path": "calm/sequence.py",
112
+ "sha256": "e76029c065a5982cb5f260984025b53efef4f44040ea6674d4b2417cde0ba2b7",
113
+ "language": "Python",
114
+ "lines": 49,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 19309
118
+ },
119
+ {
120
+ "path": "checkpointing.py",
121
+ "sha256": "c10e9d14d326e9611373d39bb5c394185108df2654a8fd5345011f8b37899592",
122
+ "language": "Python",
123
+ "lines": 27,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 18830
127
+ },
128
+ {
129
+ "path": "data_module.py",
130
+ "sha256": "f8543f3a2562531c40fa88b3823cd0e593c65b6c25bb754141af3f8dcb22770f",
131
+ "language": "Python",
132
+ "lines": 55,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 19961
136
+ },
137
+ {
138
+ "path": "test_pipeline.py",
139
+ "sha256": "0749a88e16ba19a3e5f6e6a1bd1cce3a1a87b3fb9c18481590a329991a643719",
140
+ "language": "Python",
141
+ "lines": 78,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 20616
145
+ },
146
+ {
147
+ "path": "test_sequence.py",
148
+ "sha256": "55881a88c3f9003ae01fc0c46922f6980a5d4f0f91b1f2a8f6714078276e844d",
149
+ "language": "Python",
150
+ "lines": 10,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 17847
154
+ },
155
+ {
156
+ "path": "training.py",
157
+ "sha256": "6eea528de7724320eee5deed7eb6caf231c5c2c816b71aa99c06b2f735f3f1bf",
158
+ "language": "Python",
159
+ "lines": 141,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 23101
163
+ }
164
+ ]
165
+ }
manifests/f7/zenodo__21207822.json ADDED
@@ -0,0 +1,156 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:21207822",
4
+ "url": "https://doi.org/10.5281/zenodo.21207822",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "3b514e493d0111624545786d182f56b605a663394c09d4fa09a8d05566b44faf",
14
+ "language": "License",
15
+ "lines": 21,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8013
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "19d75eb16e857795fd8cb8c98c0a8b8922563f5ca6df0df08b0425cb374b3e27",
23
+ "language": "Text",
24
+ "lines": 11,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2300
28
+ },
29
+ {
30
+ "path": "Scripts/Alpha.R",
31
+ "sha256": "904f243aa3dd057bd0313ccc4c6fc66c8997dcb4486db6f1f66da7d8290d3bb7",
32
+ "language": "R",
33
+ "lines": 158,
34
+ "truncated": false,
35
+ "block": 4,
36
+ "row": 659
37
+ },
38
+ {
39
+ "path": "Scripts/Aperiod.R",
40
+ "sha256": "70ec1643f24747bbfe02bd6902b4d98aa5cbb026819ce8fd3d462cbfcc1753ea",
41
+ "language": "R",
42
+ "lines": 131,
43
+ "truncated": false,
44
+ "block": 4,
45
+ "row": 586
46
+ },
47
+ {
48
+ "path": "Scripts/Beta.R",
49
+ "sha256": "26122d9a87d0a8f5c21d377211700b82af76c2932e715fc8bc02ef163d8e1957",
50
+ "language": "R",
51
+ "lines": 158,
52
+ "truncated": false,
53
+ "block": 4,
54
+ "row": 656
55
+ },
56
+ {
57
+ "path": "Scripts/CWB.R",
58
+ "sha256": "31e42ab0c7f61498b11a6b756bea7a4e282723a9d880135bdc7eb7788c9f3218",
59
+ "language": "R",
60
+ "lines": 271,
61
+ "truncated": false,
62
+ "block": 4,
63
+ "row": 859
64
+ },
65
+ {
66
+ "path": "Scripts/Covariation.R",
67
+ "sha256": "d453cc723b7c21ec31d6c9f03247f31cdc21bd6bc08a8223aa3fad7c233c9ff4",
68
+ "language": "R",
69
+ "lines": 357,
70
+ "truncated": false,
71
+ "block": 4,
72
+ "row": 960
73
+ },
74
+ {
75
+ "path": "Scripts/Delta.R",
76
+ "sha256": "3bcd4cce99f1431607f9cb9f8c03e9cf606952746a62ba6d81afb6e178febf43",
77
+ "language": "R",
78
+ "lines": 168,
79
+ "truncated": false,
80
+ "block": 4,
81
+ "row": 679
82
+ },
83
+ {
84
+ "path": "Scripts/MIST.R",
85
+ "sha256": "55fc276029c75b16b1e4d8ce72e516ca72de9d3895989df073e0fa626afa5768",
86
+ "language": "R",
87
+ "lines": 79,
88
+ "truncated": false,
89
+ "block": 4,
90
+ "row": 461
91
+ },
92
+ {
93
+ "path": "Scripts/Offset.R",
94
+ "sha256": "aa84823686576a8973535290ac7d4ca59615144b8a0c13a967ff6ccd076e5b4c",
95
+ "language": "R",
96
+ "lines": 158,
97
+ "truncated": false,
98
+ "block": 4,
99
+ "row": 655
100
+ },
101
+ {
102
+ "path": "Scripts/PSD.R",
103
+ "sha256": "cfd793094e1f6978e8b1c9e518bab229551956b7cf6faa6c192e29483df4de6d",
104
+ "language": "R",
105
+ "lines": 104,
106
+ "truncated": false,
107
+ "block": 4,
108
+ "row": 509
109
+ },
110
+ {
111
+ "path": "Scripts/R2.R",
112
+ "sha256": "760e972d49fe7459acbf7a632fe6eda032ade194dba953fe21c2cb0a2cecf5e0",
113
+ "language": "R",
114
+ "lines": 129,
115
+ "truncated": false,
116
+ "block": 4,
117
+ "row": 576
118
+ },
119
+ {
120
+ "path": "Scripts/Stress.R",
121
+ "sha256": "7efe3ecd792c18152bf87cbc6755e0ce2eb75bd22ab87b338e3971561b18645a",
122
+ "language": "R",
123
+ "lines": 48,
124
+ "truncated": false,
125
+ "block": 4,
126
+ "row": 310
127
+ },
128
+ {
129
+ "path": "Scripts/Theta.R",
130
+ "sha256": "e3a42d66b5b9ef71df1e927d5e273a2d6e106e37c6fa533c7b421ebbafc693f2",
131
+ "language": "R",
132
+ "lines": 131,
133
+ "truncated": false,
134
+ "block": 4,
135
+ "row": 592
136
+ },
137
+ {
138
+ "path": "Scripts/aperiodic_preprocessing.py",
139
+ "sha256": "4718f05b30538042083944ef27dc56eae86b8d460d27e5374d0632d5bdb61111",
140
+ "language": "Python",
141
+ "lines": 120,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 22812
145
+ },
146
+ {
147
+ "path": "Scripts/eeg_cleaning.m",
148
+ "sha256": "7fe3fd12dad1ac20eb04c06b61c83ae294ff8435166200ed46c2a9407cd1f2b2",
149
+ "language": "MATLAB",
150
+ "lines": 24,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 9591
154
+ }
155
+ ]
156
+ }
manifests/f8/github.com__precimed__gsa-mixer.json ADDED
@@ -0,0 +1,948 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/precimed/gsa-mixer",
4
+ "url": "https://github.com/precimed/gsa-mixer",
5
+ "host": "github.com",
6
+ "commit": "f534e7fbb1da56739f6592a326ae17ee89cffb31",
7
+ "license": "GPL-3.0",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "db577a83cb12a0be806cd166a31fa86335768c7981424181028a1a1bfbac0c62",
14
+ "language": "License",
15
+ "lines": 219,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8166
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "630e5cb28506474b6b248d32f26863a6d54080d3e9be4f61a81c7022b09ba0b8",
23
+ "language": "Text",
24
+ "lines": 77,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2536
28
+ },
29
+ {
30
+ "path": "annotations/data/maketest.sh",
31
+ "sha256": "5d76ea92df2561b1e9b473d21c50c1d6b604aa808f8fc464bdf3bd9b4c36a145",
32
+ "language": "Shell",
33
+ "lines": 19,
34
+ "truncated": false,
35
+ "block": 4,
36
+ "row": 1674
37
+ },
38
+ {
39
+ "path": "annotations/notebooks/.ipynb_checkpoints/cmm_gadient_opt-checkpoint.ipynb",
40
+ "sha256": "e62677726dc1830c2ee5980b345bae062c500af225f054ef6b3ba6c356f4a118",
41
+ "language": "Jupyter",
42
+ "lines": 235,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 7498
46
+ },
47
+ {
48
+ "path": "annotations/notebooks/bic.ipynb",
49
+ "sha256": "d7a46577c1acffbe3d7508ab3e1377ebc25c28e15b54ab41d6a92f51edc0d636",
50
+ "language": "Jupyter",
51
+ "lines": 53,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 7147
55
+ },
56
+ {
57
+ "path": "annotations/notebooks/cmm_gadient_opt.ipynb",
58
+ "sha256": "93fa4ad6238a2e0806cb3a79c505d0efaecb040416e6c959e6a3f25902adcecc",
59
+ "language": "Jupyter",
60
+ "lines": 300,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 7592
64
+ },
65
+ {
66
+ "path": "annotations/notebooks/compare_opt_parameters.ipynb",
67
+ "sha256": "c6792cc1b10ed9382d743222e30a69f0f30aa4304ee5f4232c2bfd52e538ff18",
68
+ "language": "Jupyter",
69
+ "lines": 236,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 7502
73
+ },
74
+ {
75
+ "path": "annotations/notebooks/e1.ipynb",
76
+ "sha256": "c8f045980006eb8831fddeaca6fdcc9259d505a6cee34c7bc02056941e682d88",
77
+ "language": "Jupyter",
78
+ "lines": 753,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 7813
82
+ },
83
+ {
84
+ "path": "annotations/notebooks/e1_june.ipynb",
85
+ "sha256": "da1562f5820f01a9976589bc8b33fa626162d97094281cbef78d7f8d20c08e68",
86
+ "language": "Jupyter",
87
+ "lines": 224,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 7516
91
+ },
92
+ {
93
+ "path": "annotations/notebooks/e1_real.ipynb",
94
+ "sha256": "70f5e7b112a17528fc8fbb85d1f81d768002c2d641ffeb1b1733dd23bac47ef0",
95
+ "language": "Jupyter",
96
+ "lines": 182,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 7390
100
+ },
101
+ {
102
+ "path": "annotations/notebooks/experiment_12.ipynb",
103
+ "sha256": "6f013a9b8590179e802b1c512b00ca3fe5f1ee372645ef6430e876e7641c40db",
104
+ "language": "Jupyter",
105
+ "lines": 88,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 7334
109
+ },
110
+ {
111
+ "path": "annotations/notebooks/figures.ipynb",
112
+ "sha256": "ee7dad118e7703571c66ca4c1cbd070eb514f36ccca227c792530d579f722e59",
113
+ "language": "Jupyter",
114
+ "lines": 122,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 7290
118
+ },
119
+ {
120
+ "path": "annotations/notebooks/figures_paper.ipynb",
121
+ "sha256": "a25a42918b2ff0ac5e79eb7917c1f13cf3763588f456bcff9e0e77514a616de5",
122
+ "language": "Jupyter",
123
+ "lines": 750,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 7816
127
+ },
128
+ {
129
+ "path": "annotations/notebooks/qq_test.ipynb",
130
+ "sha256": "7e69454648a3223b741218cd25360cc7e253f029a10756987347cece904977e9",
131
+ "language": "Jupyter",
132
+ "lines": 210,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 7496
136
+ },
137
+ {
138
+ "path": "annotations/notebooks/regional_cmma_concept.ipynb",
139
+ "sha256": "fb16557e03c16cae1079fe78346000353cbdf9ea884cd95e0dc475624a516259",
140
+ "language": "Jupyter",
141
+ "lines": 48,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 7052
145
+ },
146
+ {
147
+ "path": "annotations/notebooks/sigma2_from_causal.ipynb",
148
+ "sha256": "41eff91f8d882927d81e4bfd039bd360983a946edd57847f3fd8105ab5548cdb",
149
+ "language": "Jupyter",
150
+ "lines": 43,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 7070
154
+ },
155
+ {
156
+ "path": "annotations/src/annot2annomat.py",
157
+ "sha256": "b56ed4e6be89bafc6022a66c14fcf93df5d1a748638da78b287869abb4a784d3",
158
+ "language": "Python",
159
+ "lines": 45,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 19829
163
+ },
164
+ {
165
+ "path": "annotations/src/c/_cmmcost_omp.c",
166
+ "sha256": "dadd47cc8fc7f19b76883954632ffad5839cd26d22c576669202b8fe875bc848",
167
+ "language": "C",
168
+ "lines": 701,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 304
172
+ },
173
+ {
174
+ "path": "annotations/src/c/_cmmcost_omp.h",
175
+ "sha256": "9fc66bdd8ce848f661974b06516f4c377e3be7504c9699e9f1bd3698c6707a92",
176
+ "language": "C/C++",
177
+ "lines": 72,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 3924
181
+ },
182
+ {
183
+ "path": "annotations/src/c/setup_cmmcost_omp.py",
184
+ "sha256": "14d7b8f24bfb2f2e2b7d19714880c4f3a8e7b2c61858224ea035847f59b29602",
185
+ "language": "Python",
186
+ "lines": 19,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 18632
190
+ },
191
+ {
192
+ "path": "annotations/src/c/setup_cmmcost_omp_abel.py",
193
+ "sha256": "8b0db9500298839f4abffc5d8c7914d0f5ee6bcf5c99802dad5dd10faf534239",
194
+ "language": "Python",
195
+ "lines": 19,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 18714
199
+ },
200
+ {
201
+ "path": "annotations/src/c/test_cmmcost.py",
202
+ "sha256": "5597f7a429688d4a09267ef11ce35fccfd2589cdfaaf628627eadfe6fb18ee0b",
203
+ "language": "Python",
204
+ "lines": 205,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 25033
208
+ },
209
+ {
210
+ "path": "annotations/src/cfg/e1/make_e1_cfg.sh",
211
+ "sha256": "3f05b4a3913dab7b3ad6d298018928a16a511538b42e32a24e49d5eaadd139e5",
212
+ "language": "Shell",
213
+ "lines": 22,
214
+ "truncated": false,
215
+ "block": 4,
216
+ "row": 1717
217
+ },
218
+ {
219
+ "path": "annotations/src/knownGene2annot.py",
220
+ "sha256": "f4505b52d411fe3317066ec091212d56775e9b27a27e161bb4d60f5924fa6118",
221
+ "language": "Python",
222
+ "lines": 187,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 25299
226
+ },
227
+ {
228
+ "path": "annotations/src/ld_informed_annot.py",
229
+ "sha256": "006ec48d7cac4ea69d82ece0fbe7dcb0f6baf93d229b0040293e8f198fddd09a",
230
+ "language": "Python",
231
+ "lines": 114,
232
+ "truncated": false,
233
+ "block": 3,
234
+ "row": 22854
235
+ },
236
+ {
237
+ "path": "annotations/src/makeinput.py",
238
+ "sha256": "c085227b9fa7d7ebf305a54c460b7412a96da2a291b3632a516a7465808db6d2",
239
+ "language": "Python",
240
+ "lines": 218,
241
+ "truncated": false,
242
+ "block": 3,
243
+ "row": 25052
244
+ },
245
+ {
246
+ "path": "annotations/src/optimize.py",
247
+ "sha256": "e70ef0add58a9d3595a6276e40302092b99da6b784e1d6eb06101401e087ee11",
248
+ "language": "Python",
249
+ "lines": 776,
250
+ "truncated": false,
251
+ "block": 3,
252
+ "row": 27666
253
+ },
254
+ {
255
+ "path": "annotations/src/run/run_bad_qual.sh",
256
+ "sha256": "a4986ac2dcfad91b40ab4baccfcfae45dd9c8c4daa10a838d8adff92eabb5c12",
257
+ "language": "Shell",
258
+ "lines": 8,
259
+ "truncated": false,
260
+ "block": 4,
261
+ "row": 1342
262
+ },
263
+ {
264
+ "path": "annotations/src/run/run_hsq_i.sh",
265
+ "sha256": "daa2844f38d977a5286f59feb9bbc8d884b80eb33e12f8275dcaeebc017dfecb",
266
+ "language": "Shell",
267
+ "lines": 14,
268
+ "truncated": false,
269
+ "block": 4,
270
+ "row": 1415
271
+ },
272
+ {
273
+ "path": "annotations/src/run/run_makeinput.e1_real.sh",
274
+ "sha256": "f46235351ea4f72c1ca1651dea2020300bbb5387aa22238edcf64880b0c5c7d0",
275
+ "language": "Shell",
276
+ "lines": 25,
277
+ "truncated": false,
278
+ "block": 4,
279
+ "row": 1657
280
+ },
281
+ {
282
+ "path": "annotations/src/run/run_optimize.e1.sh",
283
+ "sha256": "5210571265f46ba2ba965acd7481d25b017e8656a80fc4467a1faa1a04019bb9",
284
+ "language": "Shell",
285
+ "lines": 40,
286
+ "truncated": false,
287
+ "block": 4,
288
+ "row": 1800
289
+ },
290
+ {
291
+ "path": "annotations/src/run/run_optimize.e1_real.sh",
292
+ "sha256": "f81a6bb4103194345a3bad2f4d1a5b223ed959ad8642f78d75f08c2cd9cee9ef",
293
+ "language": "Shell",
294
+ "lines": 37,
295
+ "truncated": false,
296
+ "block": 4,
297
+ "row": 1781
298
+ },
299
+ {
300
+ "path": "annotations/src/uniq_annot.py",
301
+ "sha256": "d3ea35fae9598387474110ed424906d60c1dfd5b14c5f336e8f3cebe20055942",
302
+ "language": "Python",
303
+ "lines": 66,
304
+ "truncated": false,
305
+ "block": 3,
306
+ "row": 20797
307
+ },
308
+ {
309
+ "path": "docker/scripts/apt_get_essential.sh",
310
+ "sha256": "d71e42b1ce44a960e09e268af0cad6633a9cc2f14b48587453e8e54e39def3c5",
311
+ "language": "Shell",
312
+ "lines": 48,
313
+ "truncated": false,
314
+ "block": 4,
315
+ "row": 1774
316
+ },
317
+ {
318
+ "path": "docker/scripts/from_docker_image.sh",
319
+ "sha256": "6508516d776622fc5e2fdca0a4e3318b27516aa9767d847289c5e56aa547d28b",
320
+ "language": "Shell",
321
+ "lines": 40,
322
+ "truncated": false,
323
+ "block": 4,
324
+ "row": 1760
325
+ },
326
+ {
327
+ "path": "docker/scripts/install_magma.sh",
328
+ "sha256": "eb1a9947b1e12aa931279060fb5347576a5bcd10c373a1bc8787d2a5765d14f9",
329
+ "language": "Shell",
330
+ "lines": 5,
331
+ "truncated": false,
332
+ "block": 4,
333
+ "row": 1344
334
+ },
335
+ {
336
+ "path": "docker/scripts/install_mambaforge.sh",
337
+ "sha256": "97a1e2779c02bcc9aa33fdf428c1807d29fed1587faef371c59cf700260a9495",
338
+ "language": "Shell",
339
+ "lines": 10,
340
+ "truncated": false,
341
+ "block": 4,
342
+ "row": 1419
343
+ },
344
+ {
345
+ "path": "docker/scripts/install_plink.sh",
346
+ "sha256": "ab37a0a4ec515136e97151de484002f3ea781b40aec8ca326d2ba4d6ceb2e487",
347
+ "language": "Shell",
348
+ "lines": 9,
349
+ "truncated": false,
350
+ "block": 4,
351
+ "row": 1381
352
+ },
353
+ {
354
+ "path": "docker/scripts/install_plink2.sh",
355
+ "sha256": "c1fed2158a2d7cb71be1b80e9d6cd42422fe3cb80e453bcb6f52a1d3eb304b6c",
356
+ "language": "Shell",
357
+ "lines": 12,
358
+ "truncated": false,
359
+ "block": 4,
360
+ "row": 1397
361
+ },
362
+ {
363
+ "path": "docker/scripts/install_simu.sh",
364
+ "sha256": "aaa88aa9ed8d3606ff0701cf500b64c2bba06d7f421dcf9eb5073a1dc29a65af",
365
+ "language": "Shell",
366
+ "lines": 4,
367
+ "truncated": false,
368
+ "block": 4,
369
+ "row": 1329
370
+ },
371
+ {
372
+ "path": "manuscript/bivar_mixer/mixer_gen.py",
373
+ "sha256": "1f30819a6c2c210388eb87eb46f5eb6cd70177a17a4a4c5adf62ac640972dd81",
374
+ "language": "Python",
375
+ "lines": 98,
376
+ "truncated": false,
377
+ "block": 3,
378
+ "row": 21146
379
+ },
380
+ {
381
+ "path": "manuscript/bivar_mixer/mixer_simu.py",
382
+ "sha256": "6267dff936a08299900b0120e2373ff75a4bc1458471ecdfae51d4e94671b74b",
383
+ "language": "Python",
384
+ "lines": 283,
385
+ "truncated": false,
386
+ "block": 3,
387
+ "row": 25815
388
+ },
389
+ {
390
+ "path": "manuscript/bivar_mixer/perf.py",
391
+ "sha256": "be2df25bb9d6560f3834c90437e6a438499458e969b4b0fe8a3f1d8b97d8ed45",
392
+ "language": "Python",
393
+ "lines": 23,
394
+ "truncated": false,
395
+ "block": 3,
396
+ "row": 19038
397
+ },
398
+ {
399
+ "path": "manuscript/bivar_mixer/saga_bgmg_script.sh",
400
+ "sha256": "5124ed3f1262eea8aa0c84bdb224c47d4cdd5adf380a8f3773c8a2fb88708e87",
401
+ "language": "Shell",
402
+ "lines": 54,
403
+ "truncated": false,
404
+ "block": 4,
405
+ "row": 1984
406
+ },
407
+ {
408
+ "path": "manuscript/bivar_mixer/saga_ugmg_script.sh",
409
+ "sha256": "b61bf75a150e22dc12efae5cca5bf385f8733ee58d516fcfcfa8100f5a718200",
410
+ "language": "Shell",
411
+ "lines": 50,
412
+ "truncated": false,
413
+ "block": 4,
414
+ "row": 1930
415
+ },
416
+ {
417
+ "path": "manuscript/bivar_mixer/tsd_bgmg_script.sh",
418
+ "sha256": "7e5de5ecd4c65bc29f5d03667479858c91f6da08fa5f6564eaf96618692dc6c7",
419
+ "language": "Shell",
420
+ "lines": 56,
421
+ "truncated": false,
422
+ "block": 4,
423
+ "row": 1988
424
+ },
425
+ {
426
+ "path": "manuscript/bivar_mixer/tsd_ugmg_script.sh",
427
+ "sha256": "dcbb642caee94917b4a4ca3ad25f59e9aaef666cc01673276b39b2c2e6ab3341",
428
+ "language": "Shell",
429
+ "lines": 53,
430
+ "truncated": false,
431
+ "block": 4,
432
+ "row": 1937
433
+ },
434
+ {
435
+ "path": "manuscript/bivar_mixer/xsede_snps_script.sh",
436
+ "sha256": "57ffa3ec88af5865835ef27b57a401b36c4982ea5c80f97b621e798bcb5a477d",
437
+ "language": "Shell",
438
+ "lines": 27,
439
+ "truncated": false,
440
+ "block": 4,
441
+ "row": 1811
442
+ },
443
+ {
444
+ "path": "manuscript/gsa_mixer/ldak-gbat/make_extract_list.py",
445
+ "sha256": "4924a4e92491f2fb5c7a106a12d0b12fca3286cb74c8f2c14c5c740f2e71dfab",
446
+ "language": "Python",
447
+ "lines": 29,
448
+ "truncated": false,
449
+ "block": 3,
450
+ "row": 19602
451
+ },
452
+ {
453
+ "path": "precimed/bivar_mixer/cli.py",
454
+ "sha256": "69b975a1ea835943cb9537b20d44e14341536c00dc34dc761c8fb17c1cf2f107",
455
+ "language": "Python",
456
+ "lines": 533,
457
+ "truncated": false,
458
+ "block": 3,
459
+ "row": 27742
460
+ },
461
+ {
462
+ "path": "precimed/bivar_mixer/figures.py",
463
+ "sha256": "c110f5e44a571cd6b2691f9a416509a937013eff5e26b3c495c508a52ece5f3e",
464
+ "language": "Python",
465
+ "lines": 718,
466
+ "truncated": false,
467
+ "block": 3,
468
+ "row": 27853
469
+ },
470
+ {
471
+ "path": "precimed/bivar_mixer/utils.py",
472
+ "sha256": "437e438501b6ad8cb9349ffa27f2752be08a8d71a6a1df13b522ae1706829284",
473
+ "language": "Python",
474
+ "lines": 802,
475
+ "truncated": false,
476
+ "block": 3,
477
+ "row": 27829
478
+ },
479
+ {
480
+ "path": "precimed/bivar_mixer/utils_test.py",
481
+ "sha256": "768ed74db83be46cbaf93c57157cf6d7ece6141f55adcdcb4de824ad5f0b691f",
482
+ "language": "Python",
483
+ "lines": 152,
484
+ "truncated": false,
485
+ "block": 3,
486
+ "row": 24653
487
+ },
488
+ {
489
+ "path": "precimed/common/libbgmg.py",
490
+ "sha256": "24f599dc7641a12eb25a9af8a7a34b46e75c9326a6361176dcbd8ff589bcfbe0",
491
+ "language": "Python",
492
+ "lines": 566,
493
+ "truncated": false,
494
+ "block": 3,
495
+ "row": 27690
496
+ },
497
+ {
498
+ "path": "precimed/common/utils.py",
499
+ "sha256": "703553f47f2d3126e94b6ddbde58907e861742e7cea6f419c4c1e2e6ca1129f1",
500
+ "language": "Python",
501
+ "lines": 73,
502
+ "truncated": false,
503
+ "block": 3,
504
+ "row": 20755
505
+ },
506
+ {
507
+ "path": "precimed/common/utils_cli.py",
508
+ "sha256": "c906014b07feac50189ccfd1b71319ab05b75a8240239d89c94ebcdf25b9c30f",
509
+ "language": "Python",
510
+ "lines": 184,
511
+ "truncated": false,
512
+ "block": 3,
513
+ "row": 25984
514
+ },
515
+ {
516
+ "path": "precimed/common/utils_test.py",
517
+ "sha256": "be30cdd2e730f30f2f2bdc89b92f010955e877cb30140b7170dc1eacb3672473",
518
+ "language": "Python",
519
+ "lines": 31,
520
+ "truncated": false,
521
+ "block": 3,
522
+ "row": 19879
523
+ },
524
+ {
525
+ "path": "precimed/gsa_mixer/cli.py",
526
+ "sha256": "984c87bda0dc348ac907b6ce8a2316f90eb3923d891cadf3f75543a5f0504650",
527
+ "language": "Python",
528
+ "lines": 800,
529
+ "truncated": false,
530
+ "block": 3,
531
+ "row": 27972
532
+ },
533
+ {
534
+ "path": "precimed/gsa_mixer/utils.py",
535
+ "sha256": "c09974e014c6a33c90df2c50536a7ffd6599c1cf7dd2da29d8b9d36da92654b8",
536
+ "language": "Python",
537
+ "lines": 626,
538
+ "truncated": false,
539
+ "block": 3,
540
+ "row": 27657
541
+ },
542
+ {
543
+ "path": "precimed/gsa_mixer/utils_test.py",
544
+ "sha256": "50d2c003d53ffd72dbe68cfa8663185a189d61cddece0fe98089d3c3e2e60f36",
545
+ "language": "Python",
546
+ "lines": 173,
547
+ "truncated": false,
548
+ "block": 3,
549
+ "row": 25070
550
+ },
551
+ {
552
+ "path": "precimed/mixer-test/gitrevert.sh",
553
+ "sha256": "ea0b1c93fad4bc2ad26685aa17389f4825c72ce9a298d49d1201bd7d63ac13dc",
554
+ "language": "Shell",
555
+ "lines": 9,
556
+ "truncated": false,
557
+ "block": 4,
558
+ "row": 1395
559
+ },
560
+ {
561
+ "path": "precimed/mixer-test/test_cli.py",
562
+ "sha256": "f26b34692d77aee29c5d14319a3be3b46457a64e50d499f0ef846eb4c3e3ab70",
563
+ "language": "Python",
564
+ "lines": 293,
565
+ "truncated": false,
566
+ "block": 3,
567
+ "row": 25967
568
+ },
569
+ {
570
+ "path": "precimed/mixer-test/test_dev_cli.py",
571
+ "sha256": "d83ecf621682259d7a8a446634a39059f6e0d64f9b6ef6ab071c8785c2ff4e60",
572
+ "language": "Python",
573
+ "lines": 551,
574
+ "truncated": false,
575
+ "block": 3,
576
+ "row": 27259
577
+ },
578
+ {
579
+ "path": "precimed/mixer-test/test_ld.py",
580
+ "sha256": "3fea52cfe1210c88a430d788c189bb55ba4f9b91a7b3eecdbd0e196c7c4bd0f4",
581
+ "language": "Python",
582
+ "lines": 76,
583
+ "truncated": false,
584
+ "block": 3,
585
+ "row": 22899
586
+ },
587
+ {
588
+ "path": "precimed/mixer-test/test_parse.py",
589
+ "sha256": "6b9d973502e9dcb5d671cf43ee60a254a40614474b2b7f745c1f8ac7fe66e916",
590
+ "language": "Python",
591
+ "lines": 96,
592
+ "truncated": false,
593
+ "block": 3,
594
+ "row": 22332
595
+ },
596
+ {
597
+ "path": "precimed/mixer.py",
598
+ "sha256": "47105ceb927553a9ce3da8389d1d9ba471c7712084355d79a7662e3de9ceb151",
599
+ "language": "Python",
600
+ "lines": 52,
601
+ "truncated": false,
602
+ "block": 3,
603
+ "row": 21330
604
+ },
605
+ {
606
+ "path": "precimed/mixer_dev.py",
607
+ "sha256": "dde7bb355e86949c03e77bc185cd2f11cd09e0e80ed517a2efc8dbd63402a674",
608
+ "language": "Python",
609
+ "lines": 66,
610
+ "truncated": false,
611
+ "block": 3,
612
+ "row": 23266
613
+ },
614
+ {
615
+ "path": "precimed/mixer_dev/cli.py",
616
+ "sha256": "78017ffe14d03b76ec740651c44420347b7180396d10efb347776d21d4049c2c",
617
+ "language": "Python",
618
+ "lines": 871,
619
+ "truncated": false,
620
+ "block": 3,
621
+ "row": 28008
622
+ },
623
+ {
624
+ "path": "precimed/mixer_dev/utils.py",
625
+ "sha256": "124b0f0d4d983b6ce62b2dafa29bfcf933f391c1711ef84b6c239ce88e0e4bea",
626
+ "language": "Python",
627
+ "lines": 444,
628
+ "truncated": false,
629
+ "block": 3,
630
+ "row": 27175
631
+ },
632
+ {
633
+ "path": "precimed/mixer_dev/utils_obsolete.py",
634
+ "sha256": "c92403ec7d62d953aec73f83abb2560c0e0bc6064101c06014e3ef38b345cc8d",
635
+ "language": "Python",
636
+ "lines": 94,
637
+ "truncated": false,
638
+ "block": 3,
639
+ "row": 22301
640
+ },
641
+ {
642
+ "path": "precimed/mixer_dev/utils_test.py",
643
+ "sha256": "1e030d9291c405940aac9abcb9c36e7b52dc399d2323d496a6cba92461999259",
644
+ "language": "Python",
645
+ "lines": 159,
646
+ "truncated": false,
647
+ "block": 3,
648
+ "row": 24964
649
+ },
650
+ {
651
+ "path": "precimed/mixer_figures.py",
652
+ "sha256": "a46118e8df73a76d5e5e212a24eb384233ef5702955c37b284a8a977c96a6e77",
653
+ "language": "Python",
654
+ "lines": 47,
655
+ "truncated": false,
656
+ "block": 3,
657
+ "row": 21074
658
+ },
659
+ {
660
+ "path": "precimed/version.py",
661
+ "sha256": "c7c62a1a3eb2c26fc40625f78db490bd862cef8597e0bcc3880380c2c1501d50",
662
+ "language": "Python",
663
+ "lines": 21,
664
+ "truncated": false,
665
+ "block": 3,
666
+ "row": 18899
667
+ },
668
+ {
669
+ "path": "src/FastDifferentialCoding/fastdelta.c",
670
+ "sha256": "2ea074c653a6bb755c4c4433c96060ed3e72f0e1ae5076e7246eba07f044394d",
671
+ "language": "C",
672
+ "lines": 100,
673
+ "truncated": false,
674
+ "block": 3,
675
+ "row": 122
676
+ },
677
+ {
678
+ "path": "src/FastDifferentialCoding/fastdelta.h",
679
+ "sha256": "4a014e0413d500603c1017a262ab891ada1df2e036c462b89abc5db3c955167c",
680
+ "language": "C/C++",
681
+ "lines": 49,
682
+ "truncated": false,
683
+ "block": 3,
684
+ "row": 3751
685
+ },
686
+ {
687
+ "path": "src/SIMDxorshift/simdaesdragontamer.h",
688
+ "sha256": "45e93890bafaf6fefb648fdddd068c5550c7252be057bf4658b5dfdff20c0680",
689
+ "language": "C/C++",
690
+ "lines": 85,
691
+ "truncated": false,
692
+ "block": 3,
693
+ "row": 3897
694
+ },
695
+ {
696
+ "path": "src/SIMDxorshift/simdxorshift128plus.c",
697
+ "sha256": "f2c4973203f665c14dc1a94cfa5d628d3956aaf9728d3409574a9dc716a34442",
698
+ "language": "C",
699
+ "lines": 192,
700
+ "truncated": false,
701
+ "block": 3,
702
+ "row": 176
703
+ },
704
+ {
705
+ "path": "src/SIMDxorshift/simdxorshift128plus.h",
706
+ "sha256": "1dfbdc474c1bfc62d8d46624d17e4d2f8845f951d56560b02fb7248d02cf8585",
707
+ "language": "C/C++",
708
+ "lines": 126,
709
+ "truncated": false,
710
+ "block": 3,
711
+ "row": 3992
712
+ },
713
+ {
714
+ "path": "src/SIMDxorshift/xorshift128plus.c",
715
+ "sha256": "9d568d6bf79050d445ec7d43cb9d7ee3d34addcf6e0648da6d0e6323c2498d8f",
716
+ "language": "C",
717
+ "lines": 81,
718
+ "truncated": false,
719
+ "block": 3,
720
+ "row": 87
721
+ },
722
+ {
723
+ "path": "src/SIMDxorshift/xorshift128plus.h",
724
+ "sha256": "eaaf08827edcfeadd842feac4c9ad4904025cd7bf27cb0d597ff18c6ca137941",
725
+ "language": "C/C++",
726
+ "lines": 65,
727
+ "truncated": false,
728
+ "block": 3,
729
+ "row": 3767
730
+ },
731
+ {
732
+ "path": "src/TurboPFor/bitutil.c",
733
+ "sha256": "b6ceeabef3a87e0f7d193752b7380961e94ee6111d1695ac279acdc422556406",
734
+ "language": "C",
735
+ "lines": 466,
736
+ "truncated": false,
737
+ "block": 3,
738
+ "row": 292
739
+ },
740
+ {
741
+ "path": "src/TurboPFor/bitutil.h",
742
+ "sha256": "aa6cee16766969c6e80b95b686d6a449c728e4be119a47fd94223e810235fe32",
743
+ "language": "C/C++",
744
+ "lines": 311,
745
+ "truncated": false,
746
+ "block": 3,
747
+ "row": 4486
748
+ },
749
+ {
750
+ "path": "src/TurboPFor/conf.h",
751
+ "sha256": "663b5c21c519b44eff9ecd153b331333396f389080342eb3b8125c5eafd40f44",
752
+ "language": "C/C++",
753
+ "lines": 243,
754
+ "truncated": false,
755
+ "block": 3,
756
+ "row": 4378
757
+ },
758
+ {
759
+ "path": "src/TurboPFor/vint.c",
760
+ "sha256": "7e0242158481e0968aa77b713ea970ac4f345ecfa5e905925677e7a60b79df59",
761
+ "language": "C",
762
+ "lines": 347,
763
+ "truncated": false,
764
+ "block": 3,
765
+ "row": 236
766
+ },
767
+ {
768
+ "path": "src/TurboPFor/vint.h",
769
+ "sha256": "5f23e247e3f5572ee3ce7da8d9fadfbd9c9e78370606e172d8e9fd86a9fe5bd9",
770
+ "language": "C/C++",
771
+ "lines": 287,
772
+ "truncated": false,
773
+ "block": 3,
774
+ "row": 4517
775
+ },
776
+ {
777
+ "path": "src/TurboPFor/vsimple.c",
778
+ "sha256": "7132d1c72840fe67e2b773c3f3d3cf4dfe82a1e3819dd392b2a54bcd583cfb7b",
779
+ "language": "C",
780
+ "lines": 522,
781
+ "truncated": false,
782
+ "block": 3,
783
+ "row": 284
784
+ },
785
+ {
786
+ "path": "src/TurboPFor/vsimple.h",
787
+ "sha256": "ac46856fbfd6f35e440be5b455a83b1aae23afd22a0c5dbe5ba7ba3d3da96312",
788
+ "language": "C/C++",
789
+ "lines": 47,
790
+ "truncated": false,
791
+ "block": 3,
792
+ "row": 3857
793
+ },
794
+ {
795
+ "path": "src/annotate_intervals.cc",
796
+ "sha256": "eedc4249057ca177bb75944c95596f42dcd2f5a30eed5bdd23db182696ee2911",
797
+ "language": "C++",
798
+ "lines": 61,
799
+ "truncated": false,
800
+ "block": 3,
801
+ "row": 1986
802
+ },
803
+ {
804
+ "path": "src/annotate_intervals.h",
805
+ "sha256": "bc4e340ccc90eb02b090db5d53d9bbd8f9142badcb7d326fa11d504e680a09d3",
806
+ "language": "C/C++",
807
+ "lines": 24,
808
+ "truncated": false,
809
+ "block": 3,
810
+ "row": 3492
811
+ },
812
+ {
813
+ "path": "src/bgmg.h",
814
+ "sha256": "c255814f0b9da3cb777303386d1f480c45497bbd81320340e2cda918f65f3a46",
815
+ "language": "C/C++",
816
+ "lines": 138,
817
+ "truncated": false,
818
+ "block": 3,
819
+ "row": 4320
820
+ },
821
+ {
822
+ "path": "src/bgmg_calculator.cc",
823
+ "sha256": "4eed28720dd3f37a90f123c0b4a2f306107fb5af99b1ac697a4d892312278303",
824
+ "language": "C++",
825
+ "lines": 1171,
826
+ "truncated": false,
827
+ "block": 3,
828
+ "row": 3275
829
+ },
830
+ {
831
+ "path": "src/bgmg_calculator.h",
832
+ "sha256": "8b45584abf37a7c7652f51f109e4468601df864464189d71108143b7fb788abd",
833
+ "language": "C/C++",
834
+ "lines": 448,
835
+ "truncated": false,
836
+ "block": 3,
837
+ "row": 4546
838
+ },
839
+ {
840
+ "path": "src/bgmg_calculator_impl.h",
841
+ "sha256": "198fb577b488b18ae8695e87102553c4c1b0d0cefc5ac259da449ead15a7a5cc",
842
+ "language": "C/C++",
843
+ "lines": 170,
844
+ "truncated": false,
845
+ "block": 3,
846
+ "row": 4160
847
+ },
848
+ {
849
+ "path": "src/bgmg_calculator_legacy.cc",
850
+ "sha256": "0922eeb5f6a7b3738ec2ff516aff208418e13337fd9eec31abbd17d9f43be923",
851
+ "language": "C++",
852
+ "lines": 1417,
853
+ "truncated": false,
854
+ "block": 3,
855
+ "row": 3285
856
+ },
857
+ {
858
+ "path": "src/bgmg_calculator_unified.cc",
859
+ "sha256": "506c86020cb4efae2859dd1b4e3480c4091e4f9bac11f62b2039dfa17e1b5df5",
860
+ "language": "C++",
861
+ "lines": 1749,
862
+ "truncated": false,
863
+ "block": 3,
864
+ "row": 3289
865
+ },
866
+ {
867
+ "path": "src/bgmg_log.cc",
868
+ "sha256": "4fc738b01a403b7926dfbf424181e346ce39bb57923ad07e0c9355e5ae454ae2",
869
+ "language": "C++",
870
+ "lines": 1,
871
+ "truncated": false,
872
+ "block": 3,
873
+ "row": 348
874
+ },
875
+ {
876
+ "path": "src/bgmg_log.h",
877
+ "sha256": "7c1a7d95eeb1fc502109a016f61348489c70b18f8cbe6cad66d6d638ec87b120",
878
+ "language": "C/C++",
879
+ "lines": 143,
880
+ "truncated": false,
881
+ "block": 3,
882
+ "row": 4014
883
+ },
884
+ {
885
+ "path": "src/bgmg_main.cc",
886
+ "sha256": "f78ed99d408e4dbfe94a426f5e769f196f369d3b900c8f981c98c4ca9c30b4db",
887
+ "language": "C++",
888
+ "lines": 232,
889
+ "truncated": false,
890
+ "block": 3,
891
+ "row": 2933
892
+ },
893
+ {
894
+ "path": "src/bgmg_math.h",
895
+ "sha256": "ae76e9bc29fcc092c34d88e9406dfb46ce278f11eb588f99bf61b569b24d8253",
896
+ "language": "C/C++",
897
+ "lines": 215,
898
+ "truncated": false,
899
+ "block": 3,
900
+ "row": 4292
901
+ },
902
+ {
903
+ "path": "src/bgmg_parse.cc",
904
+ "sha256": "3a62cfcfbb58026d1e318aa9cc84520cdf247355079b18049278bd207ca0bc16",
905
+ "language": "C++",
906
+ "lines": 667,
907
+ "truncated": false,
908
+ "block": 3,
909
+ "row": 3217
910
+ },
911
+ {
912
+ "path": "src/bgmg_parse.h",
913
+ "sha256": "414d4438dfcc4afa58e206fd6f0cccd97a0fea0b7b9b81abaaf2d455fc6c3e53",
914
+ "language": "C/C++",
915
+ "lines": 175,
916
+ "truncated": false,
917
+ "block": 3,
918
+ "row": 4097
919
+ },
920
+ {
921
+ "path": "src/bgmg_rand.h",
922
+ "sha256": "a95e39dab833c071060f58ba5f060464b7e6e6aa2afe6dcb823d10d4ed8cc660",
923
+ "language": "C/C++",
924
+ "lines": 193,
925
+ "truncated": false,
926
+ "block": 3,
927
+ "row": 4208
928
+ },
929
+ {
930
+ "path": "src/bgmg_serialize.h",
931
+ "sha256": "50b6a5321689ad7d3d73c7f9c03683b7fea4d774ce5c3ba649ef80399bef2e3e",
932
+ "language": "C/C++",
933
+ "lines": 122,
934
+ "truncated": false,
935
+ "block": 3,
936
+ "row": 3985
937
+ },
938
+ {
939
+ "path": "src/cubature/clencurt.h",
940
+ "sha256": "015f24478885e42e71162286e67a2a6244abe7399891e013100f3590ecb01e4f",
941
+ "language": "C/C++",
942
+ "lines": 9108,
943
+ "truncated": true,
944
+ "block": 3,
945
+ "row": 4625
946
+ }
947
+ ]
948
+ }
manifests/f8/github.com__thuretlabkcl__tnf-scrnaseq-neurogenesis.json ADDED
@@ -0,0 +1,84 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/thuretlabkcl/tnf-scrnaseq-neurogenesis",
4
+ "url": "https://github.com/thuretlabkcl/TNF-scRNAseq-neurogenesis",
5
+ "host": "github.com",
6
+ "commit": "bdf43f5618a7eb675c8e753c7171e0419a88783b",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "4e77f52519101586ee87ff5edc215bb6fc080886c05dfd59189623b923b5a9e6",
14
+ "language": "License",
15
+ "lines": 21,
16
+ "truncated": false,
17
+ "block": 1,
18
+ "row": 2115
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "1e5a30281519b174f43499d056820b672461f9dc4ce3fd2ed60e34ae0f58ccdf",
23
+ "language": "Text",
24
+ "lines": 200,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2602
28
+ },
29
+ {
30
+ "path": "renv/activate.R",
31
+ "sha256": "ad17689dc13ef6dce75b1f5bed883e931f239bacd71e84ef57ede143ff6476cf",
32
+ "language": "R",
33
+ "lines": 1403,
34
+ "truncated": false,
35
+ "block": 1,
36
+ "row": 10598
37
+ },
38
+ {
39
+ "path": "scripts/00_setup.R",
40
+ "sha256": "4cd1f056425f725d9cab6a449e5192de132165454128192b3f7b8b919832d699",
41
+ "language": "R",
42
+ "lines": 159,
43
+ "truncated": false,
44
+ "block": 4,
45
+ "row": 695
46
+ },
47
+ {
48
+ "path": "scripts/01_load_and_qc.Rmd",
49
+ "sha256": "289fd37ff757d6399a099724fc9edf6df8cb9b3b06ed5bbb007fbbbb82b82c2d",
50
+ "language": "R",
51
+ "lines": 575,
52
+ "truncated": false,
53
+ "block": 4,
54
+ "row": 1059
55
+ },
56
+ {
57
+ "path": "scripts/02_normalisation_and_clustering.Rmd",
58
+ "sha256": "eef7c61db9a2097ed9e5ac05dc42886070fb1f1070ec74ea5b3a644c9347cc12",
59
+ "language": "R",
60
+ "lines": 324,
61
+ "truncated": false,
62
+ "block": 4,
63
+ "row": 896
64
+ },
65
+ {
66
+ "path": "scripts/03_analysis.Rmd",
67
+ "sha256": "12b31ad1bc30ce9eaa1f8c021e092093c3ec7e99bb877f8064ccdb5cd7797052",
68
+ "language": "R",
69
+ "lines": 1162,
70
+ "truncated": false,
71
+ "block": 4,
72
+ "row": 1190
73
+ },
74
+ {
75
+ "path": "scripts/99_run_all.R",
76
+ "sha256": "dfe0097c11514dc1bbe06167d0f88b2f52ec43ee36921b396f07ec1ed1957ece",
77
+ "language": "R",
78
+ "lines": 73,
79
+ "truncated": false,
80
+ "block": 4,
81
+ "row": 408
82
+ }
83
+ ]
84
+ }
manifests/f9/github.com__jacobgil__pytorch-grad-cam.json ADDED
@@ -0,0 +1,534 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/jacobgil/pytorch-grad-cam",
4
+ "url": "https://github.com/jacobgil/pytorch-grad-cam",
5
+ "host": "github.com",
6
+ "commit": "704393448a7b0c620ee2c2b9597723f1d7f17b3d",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "daaa1016faf5179309e91ba6b7656e0c3c36cdd1695ca1c91f215e668abc7403",
14
+ "language": "License",
15
+ "lines": 21,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8035
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "05aa6941912ae099bb19ec42ea1b94053b59f795dbbc729a4223e337ffd35c5a",
23
+ "language": "Text",
24
+ "lines": 434,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2731
28
+ },
29
+ {
30
+ "path": "cam.py",
31
+ "sha256": "839efe5f1bc42acbab766f59076a1e4d66e65a847103fed2d3c3ea5a46f95bc4",
32
+ "language": "Python",
33
+ "lines": 154,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 23528
37
+ },
38
+ {
39
+ "path": "pytorch_grad_cam/__init__.py",
40
+ "sha256": "6e909fbcd0b629d69512364a7c893d9540b90215f3d33bc50648a3a47b466eb8",
41
+ "language": "Python",
42
+ "lines": 27,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 19599
46
+ },
47
+ {
48
+ "path": "pytorch_grad_cam/ablation_cam.py",
49
+ "sha256": "7b6bbe92066d804fa5d58a468f033225da0aacfebe59f279f02cc92b16489110",
50
+ "language": "Python",
51
+ "lines": 150,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 23939
55
+ },
56
+ {
57
+ "path": "pytorch_grad_cam/ablation_cam_multilayer.py",
58
+ "sha256": "c1caa6b54b3b5077b123a60dabb5205576be794df200b8e23156e408389a2c38",
59
+ "language": "Python",
60
+ "lines": 136,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 22970
64
+ },
65
+ {
66
+ "path": "pytorch_grad_cam/ablation_layer.py",
67
+ "sha256": "97b45696669fbe970112e85e45da9eaa6093e505a90866561cb0d4317ee44182",
68
+ "language": "Python",
69
+ "lines": 155,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 23670
73
+ },
74
+ {
75
+ "path": "pytorch_grad_cam/activations_and_gradients.py",
76
+ "sha256": "55c10bc8e9ea72c658f73ade7d3cad8012154a2da23e860d686ce2c52866b16a",
77
+ "language": "Python",
78
+ "lines": 67,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 20636
82
+ },
83
+ {
84
+ "path": "pytorch_grad_cam/base_cam.py",
85
+ "sha256": "22268ce7f1c86961d987699c12f9c5f25b1c8e30ff4b916065384da21a482fae",
86
+ "language": "Python",
87
+ "lines": 231,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 25117
91
+ },
92
+ {
93
+ "path": "pytorch_grad_cam/eigen_cam.py",
94
+ "sha256": "561e6937987c7de75c90a4de3d5104403b72da0a0bbcff14e34d0d5a047382ff",
95
+ "language": "Python",
96
+ "lines": 22,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 18710
100
+ },
101
+ {
102
+ "path": "pytorch_grad_cam/eigen_grad_cam.py",
103
+ "sha256": "faf8774da0164caba2669eb99912ba909c60b21f20bdb471cc0a05a1f3ea34b4",
104
+ "language": "Python",
105
+ "lines": 21,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 18677
109
+ },
110
+ {
111
+ "path": "pytorch_grad_cam/feature_factorization/deep_feature_factorization.py",
112
+ "sha256": "aebab393b4e4b23b064cad995954c41dba70778f0d422d13867760ccc2d6cb6f",
113
+ "language": "Python",
114
+ "lines": 134,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 23134
118
+ },
119
+ {
120
+ "path": "pytorch_grad_cam/fem.py",
121
+ "sha256": "d5e543e65210a6ee5d59a918a5b407c966e206423f205ba70ba65b7ceb00b940",
122
+ "language": "Python",
123
+ "lines": 45,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 20036
127
+ },
128
+ {
129
+ "path": "pytorch_grad_cam/finer_cam.py",
130
+ "sha256": "e9f5e974f11746bade53daeadbd28cd4f587136031ab3636b7c1bfafc1ef6aa0",
131
+ "language": "Python",
132
+ "lines": 117,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 22607
136
+ },
137
+ {
138
+ "path": "pytorch_grad_cam/fullgrad_cam.py",
139
+ "sha256": "0d22cf2b8b862a1adcefd6e599d5e3a5aed3981335100e98a64684081c4d804b",
140
+ "language": "Python",
141
+ "lines": 94,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 22216
145
+ },
146
+ {
147
+ "path": "pytorch_grad_cam/grad_cam.py",
148
+ "sha256": "547ece721d45473b4b14c015922e6c3a0ce3d45c2144e8f93dd7654b2e108e17",
149
+ "language": "Python",
150
+ "lines": 32,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 18882
154
+ },
155
+ {
156
+ "path": "pytorch_grad_cam/grad_cam_elementwise.py",
157
+ "sha256": "9a2839b142f61c46b40f1b8900b6ed814a57fcede5b65dfdf4c5824f92aec441",
158
+ "language": "Python",
159
+ "lines": 29,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 18865
163
+ },
164
+ {
165
+ "path": "pytorch_grad_cam/grad_cam_plusplus.py",
166
+ "sha256": "53773469881a308d38e8a8256d95b8df40e23cd3a73e63e28a0775e37a5f16f8",
167
+ "language": "Python",
168
+ "lines": 35,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 19404
172
+ },
173
+ {
174
+ "path": "pytorch_grad_cam/guided_backprop.py",
175
+ "sha256": "d2c2cf4a38d1781d320774afa04a4d051e7f3af42ec6fcca1bcc6d68ae1e199a",
176
+ "language": "Python",
177
+ "lines": 100,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 21603
181
+ },
182
+ {
183
+ "path": "pytorch_grad_cam/hirescam.py",
184
+ "sha256": "da9d19081ba6ebb03d1dbb268946f6712eefcfb0dcb2a576a0c46bfa34ef4537",
185
+ "language": "Python",
186
+ "lines": 31,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 18965
190
+ },
191
+ {
192
+ "path": "pytorch_grad_cam/kpca_cam.py",
193
+ "sha256": "4efece7600494d09d7219c3ea8fa1e4d2b646fa2bd9bbd025029953354c37a69",
194
+ "language": "Python",
195
+ "lines": 21,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 18820
199
+ },
200
+ {
201
+ "path": "pytorch_grad_cam/layer_cam.py",
202
+ "sha256": "db85dd001c8fa337b74505a5897035b2d0fe4484515b198287d84d5fe764bddd",
203
+ "language": "Python",
204
+ "lines": 34,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 18958
208
+ },
209
+ {
210
+ "path": "pytorch_grad_cam/metrics/arcc.py",
211
+ "sha256": "fbc8b385b227f70fa2a74d3952ab88336bd6d9af5a7cc72981f4ce3068c36522",
212
+ "language": "Python",
213
+ "lines": 107,
214
+ "truncated": false,
215
+ "block": 3,
216
+ "row": 22127
217
+ },
218
+ {
219
+ "path": "pytorch_grad_cam/metrics/cam_mult_image.py",
220
+ "sha256": "e08563935b789a917b8b4aa9b9d4918615cb2f592988b3e78fefccc834e75771",
221
+ "language": "Python",
222
+ "lines": 37,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 19195
226
+ },
227
+ {
228
+ "path": "pytorch_grad_cam/metrics/perturbation_confidence.py",
229
+ "sha256": "c7105ca3c2d11fea8ea145448f3383484698e5435f86bce153bbc2050a86be55",
230
+ "language": "Python",
231
+ "lines": 109,
232
+ "truncated": false,
233
+ "block": 3,
234
+ "row": 21745
235
+ },
236
+ {
237
+ "path": "pytorch_grad_cam/metrics/road.py",
238
+ "sha256": "2c1302b4730a5376cb2f5ebf16dd491124a2646fd1482937d3dc3dd3a146e7cc",
239
+ "language": "Python",
240
+ "lines": 181,
241
+ "truncated": false,
242
+ "block": 3,
243
+ "row": 24409
244
+ },
245
+ {
246
+ "path": "pytorch_grad_cam/random_cam.py",
247
+ "sha256": "17c89a18e0091bcc4d31e0a8b3a2efc541bc04ff2738d5354f0f8ada75022fd7",
248
+ "language": "Python",
249
+ "lines": 21,
250
+ "truncated": false,
251
+ "block": 3,
252
+ "row": 18513
253
+ },
254
+ {
255
+ "path": "pytorch_grad_cam/refine_cam.py",
256
+ "sha256": "81f0e4b8fd099cb1f7fc6c22f4a27d8abc1795b04257d1dd83f7407a0237197e",
257
+ "language": "Python",
258
+ "lines": 47,
259
+ "truncated": false,
260
+ "block": 3,
261
+ "row": 19897
262
+ },
263
+ {
264
+ "path": "pytorch_grad_cam/score_cam.py",
265
+ "sha256": "e794b4e79b8f59b924f442251feaa5094a41b44aeea9bc4450eb0964524c762b",
266
+ "language": "Python",
267
+ "lines": 57,
268
+ "truncated": false,
269
+ "block": 3,
270
+ "row": 20429
271
+ },
272
+ {
273
+ "path": "pytorch_grad_cam/seg_eigen_cam.py",
274
+ "sha256": "416c30dd3a836c46a97b1616bac7a63a65a8ba389fd0d5292f209f24b16582ea",
275
+ "language": "Python",
276
+ "lines": 62,
277
+ "truncated": false,
278
+ "block": 3,
279
+ "row": 20555
280
+ },
281
+ {
282
+ "path": "pytorch_grad_cam/sess.py",
283
+ "sha256": "1c104329c9fe8517d1e0215553b6611a3ad3244cef8cb2153f2838cc689efa73",
284
+ "language": "Python",
285
+ "lines": 279,
286
+ "truncated": false,
287
+ "block": 3,
288
+ "row": 25885
289
+ },
290
+ {
291
+ "path": "pytorch_grad_cam/shapley_cam.py",
292
+ "sha256": "aed8244e98b2fad384c038c0cba120741b6249f26a4b431dd48acd51f86e2ce6",
293
+ "language": "Python",
294
+ "lines": 60,
295
+ "truncated": false,
296
+ "block": 3,
297
+ "row": 20520
298
+ },
299
+ {
300
+ "path": "pytorch_grad_cam/sobel_cam.py",
301
+ "sha256": "d7a3754b54a44b0f5340904e5fef203c237c617dcb4a448240ef566bf999c094",
302
+ "language": "Python",
303
+ "lines": 11,
304
+ "truncated": false,
305
+ "block": 3,
306
+ "row": 18109
307
+ },
308
+ {
309
+ "path": "pytorch_grad_cam/utils/__init__.py",
310
+ "sha256": "2b06b221403abb412f807b04996f7f4a62b0186438b221bfdcf752ae8ee12da9",
311
+ "language": "Python",
312
+ "lines": 4,
313
+ "truncated": false,
314
+ "block": 3,
315
+ "row": 17752
316
+ },
317
+ {
318
+ "path": "pytorch_grad_cam/utils/find_layers.py",
319
+ "sha256": "06369bf7af6953dafed9271952c88a4266e68e13d02607cd727efa8ccefc6824",
320
+ "language": "Python",
321
+ "lines": 30,
322
+ "truncated": false,
323
+ "block": 3,
324
+ "row": 19046
325
+ },
326
+ {
327
+ "path": "pytorch_grad_cam/utils/image.py",
328
+ "sha256": "b6c08cc15e70fcbf52e534f26b75344427a7c353f11fc1af836d3cd98a3e2f4d",
329
+ "language": "Python",
330
+ "lines": 189,
331
+ "truncated": false,
332
+ "block": 3,
333
+ "row": 24128
334
+ },
335
+ {
336
+ "path": "pytorch_grad_cam/utils/model_targets.py",
337
+ "sha256": "56bdc7e7a838f080c4fbcf4b116b196f9405d6e9736631e23f8fcb087e5c5ded",
338
+ "language": "Python",
339
+ "lines": 142,
340
+ "truncated": false,
341
+ "block": 3,
342
+ "row": 22902
343
+ },
344
+ {
345
+ "path": "pytorch_grad_cam/utils/reshape_transforms.py",
346
+ "sha256": "959b0cb20460d5d0a5cc1bfdcb913976d99f4ef8a318e947017c1a69afad03fb",
347
+ "language": "Python",
348
+ "lines": 34,
349
+ "truncated": false,
350
+ "block": 3,
351
+ "row": 19005
352
+ },
353
+ {
354
+ "path": "pytorch_grad_cam/utils/svd_on_activations.py",
355
+ "sha256": "9f025ebc0ce8ae46ea8b9bb4f8f32c1bd1146cb911f554bf9422386b743a8d2d",
356
+ "language": "Python",
357
+ "lines": 81,
358
+ "truncated": false,
359
+ "block": 3,
360
+ "row": 21463
361
+ },
362
+ {
363
+ "path": "pytorch_grad_cam/xgrad_cam.py",
364
+ "sha256": "494df3a7688032ff53630d001982ff58ab2ca46f1788ccb2718f62243d24bf09",
365
+ "language": "Python",
366
+ "lines": 32,
367
+ "truncated": false,
368
+ "block": 3,
369
+ "row": 18960
370
+ },
371
+ {
372
+ "path": "setup.py",
373
+ "sha256": "7ce1423764020ca5fd418983d7d122b62ec49d702e2162068250674bc3a51265",
374
+ "language": "Python",
375
+ "lines": 29,
376
+ "truncated": false,
377
+ "block": 3,
378
+ "row": 19041
379
+ },
380
+ {
381
+ "path": "tests/test_3d_cam_weights.py",
382
+ "sha256": "55d20da6806adcf80383d4f9a1def3cb711e5833237fbf881e1f1b01ed549216",
383
+ "language": "Python",
384
+ "lines": 51,
385
+ "truncated": false,
386
+ "block": 3,
387
+ "row": 19526
388
+ },
389
+ {
390
+ "path": "tests/test_context_release.py",
391
+ "sha256": "dde406d0b2d08f728362404e0a785066fa2ed12fd06704e3773f0c259263690c",
392
+ "language": "Python",
393
+ "lines": 69,
394
+ "truncated": false,
395
+ "block": 3,
396
+ "row": 20321
397
+ },
398
+ {
399
+ "path": "tests/test_context_release_cuda.py",
400
+ "sha256": "f97da5285ce9cfdc196fcbcdec7e682ad829c635e016d57463d6e106edf0599f",
401
+ "language": "Python",
402
+ "lines": 76,
403
+ "truncated": false,
404
+ "block": 3,
405
+ "row": 20557
406
+ },
407
+ {
408
+ "path": "tests/test_fasterrcnn_target_device.py",
409
+ "sha256": "353d0e76deeebb8e87abd12c1d7a84e3d93054801c7fea7846c0883e1dc22a99",
410
+ "language": "Python",
411
+ "lines": 52,
412
+ "truncated": false,
413
+ "block": 3,
414
+ "row": 19959
415
+ },
416
+ {
417
+ "path": "tests/test_finer_cam_correctness.py",
418
+ "sha256": "1516771b192f5f79cc49a324858b09e313379c0466bca50a73873b1500cc3a38",
419
+ "language": "Python",
420
+ "lines": 61,
421
+ "truncated": false,
422
+ "block": 3,
423
+ "row": 20107
424
+ },
425
+ {
426
+ "path": "tests/test_one_channel.py",
427
+ "sha256": "00adeca5fc0b3b2cf51f7840fc9b4691b8a6933b4c6e06f627c29c3ca698f0f0",
428
+ "language": "Python",
429
+ "lines": 47,
430
+ "truncated": false,
431
+ "block": 3,
432
+ "row": 19357
433
+ },
434
+ {
435
+ "path": "tests/test_refine_cam.py",
436
+ "sha256": "d09843f3373e3701bcf12e1c5cc441c488c71a82f8de4cdcb99b9cf47a0e2c4b",
437
+ "language": "Python",
438
+ "lines": 75,
439
+ "truncated": false,
440
+ "block": 3,
441
+ "row": 20422
442
+ },
443
+ {
444
+ "path": "tests/test_run_all_models.py",
445
+ "sha256": "e2e56a43b2b76c34459441e455b2299d9bea98102457c583f463ba82aaf30d62",
446
+ "language": "Python",
447
+ "lines": 85,
448
+ "truncated": false,
449
+ "block": 3,
450
+ "row": 20821
451
+ },
452
+ {
453
+ "path": "tests/test_sess.py",
454
+ "sha256": "64c4c0b72e1a19d209fadaf880720a66f4b0b827b96935ac9d9c117c645ec47e",
455
+ "language": "Python",
456
+ "lines": 136,
457
+ "truncated": false,
458
+ "block": 3,
459
+ "row": 22794
460
+ },
461
+ {
462
+ "path": "tests/test_svd_no_side_effect.py",
463
+ "sha256": "0a75d30c3413e9bace24c7942aaac1a69c4429d9c853377a4a19abe99ff5ccf5",
464
+ "language": "Python",
465
+ "lines": 44,
466
+ "truncated": false,
467
+ "block": 3,
468
+ "row": 19378
469
+ },
470
+ {
471
+ "path": "tutorials/CAM Metrics And Tuning Tutorial.ipynb",
472
+ "sha256": "c2345978927c33fe6b057cf9aae1d7112a27f38f00a6d32b0ee4639084673c0d",
473
+ "language": "Jupyter",
474
+ "lines": 433,
475
+ "truncated": false,
476
+ "block": 3,
477
+ "row": 7778
478
+ },
479
+ {
480
+ "path": "tutorials/Class Activation Maps for Object Detection With Faster RCNN.ipynb",
481
+ "sha256": "eee80b27552b0830aaafbb52d7a7881c25bcf06394748c9a51be4ecba7035be6",
482
+ "language": "Jupyter",
483
+ "lines": 435,
484
+ "truncated": false,
485
+ "block": 3,
486
+ "row": 7749
487
+ },
488
+ {
489
+ "path": "tutorials/Class Activation Maps for Semantic Segmentation.ipynb",
490
+ "sha256": "43d01e5a4f728428b5804bfdf89239ecff0b74bcea1f2998447bbcaef845a8ac",
491
+ "language": "Jupyter",
492
+ "lines": 135,
493
+ "truncated": false,
494
+ "block": 3,
495
+ "row": 7356
496
+ },
497
+ {
498
+ "path": "tutorials/Deep Feature Factorizations.ipynb",
499
+ "sha256": "5165053408ea385ab39d8cdda1f2f1034012768f63b729b98c051425425fedd9",
500
+ "language": "Jupyter",
501
+ "lines": 230,
502
+ "truncated": false,
503
+ "block": 3,
504
+ "row": 7646
505
+ },
506
+ {
507
+ "path": "tutorials/EigenCAM for YOLO5.ipynb",
508
+ "sha256": "8400b96c9f260da6f3aa81dec1e7082f6f1e66575df17bc8d805535c0360b1fb",
509
+ "language": "Jupyter",
510
+ "lines": 154,
511
+ "truncated": false,
512
+ "block": 3,
513
+ "row": 7382
514
+ },
515
+ {
516
+ "path": "tutorials/HuggingFace.ipynb",
517
+ "sha256": "ee3636c04cdd31dee8caca617198fb850a1db63180d392b54c43fece46727188",
518
+ "language": "Jupyter",
519
+ "lines": 550,
520
+ "truncated": false,
521
+ "block": 3,
522
+ "row": 7797
523
+ },
524
+ {
525
+ "path": "tutorials/Pixel Attribution for embeddings.ipynb",
526
+ "sha256": "fba3babd007b540b5bf7874cabe5571c6af061b4d301f0ec2ce5867a5bcf5e3f",
527
+ "language": "Jupyter",
528
+ "lines": 194,
529
+ "truncated": false,
530
+ "block": 3,
531
+ "row": 7486
532
+ }
533
+ ]
534
+ }
manifests/f9/zenodo__18508813.json ADDED
@@ -0,0 +1,30 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:18508813",
4
+ "url": "https://doi.org/10.5281/zenodo.18508813",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "CC-BY-4.0",
8
+ "license_confirmed_by": "license of the archive's record",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "MND Register and Case Control Analysis Script.R",
13
+ "sha256": "a633b8f19e8589bf0fbce292ba96bb6a0f275bf3f723f7c122d3fa32f1c3f5ec",
14
+ "language": "R",
15
+ "lines": 333,
16
+ "truncated": false,
17
+ "block": 4,
18
+ "row": 1021
19
+ },
20
+ {
21
+ "path": "Post-Mortem Cohort Analysis Script.R",
22
+ "sha256": "5597e1aef8ee7bce84500b631ba04105dcfc6583b9a3d601e575ac1943fdbb98",
23
+ "language": "R",
24
+ "lines": 318,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 1043
28
+ }
29
+ ]
30
+ }
manifests/fa/github.com__infectionmedicineproteomics__binn.json ADDED
@@ -0,0 +1,192 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/infectionmedicineproteomics/binn",
4
+ "url": "https://github.com/InfectionMedicineProteomics/BINN",
5
+ "host": "github.com",
6
+ "commit": "8bf4c33f67b6a2a8d8e196db10d65c1dc35990a3",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "aa178835a00ab2b4327dfd3f7d16d6eb46fac0c4777414924fed931066b9448a",
14
+ "language": "License",
15
+ "lines": 21,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8065
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "e0fd27c909273091934afb7de88b72564cd6574e316a8921cb32073e7d01d587",
23
+ "language": "Text",
24
+ "lines": 113,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2534
28
+ },
29
+ {
30
+ "path": "binn/__init__.py",
31
+ "sha256": "3ff11402ec15e0f6ef4e255d41ebf79ee657e703cb637efce6ef2cae890f8783",
32
+ "language": "Python",
33
+ "lines": 5,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 17713
37
+ },
38
+ {
39
+ "path": "binn/analysis/explainer.py",
40
+ "sha256": "596705f848b22e5685fc3d15d933c3485318972dbc253f73504d90e44571d185",
41
+ "language": "Python",
42
+ "lines": 387,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 26177
46
+ },
47
+ {
48
+ "path": "binn/data/__init__.py",
49
+ "sha256": "3ff11402ec15e0f6ef4e255d41ebf79ee657e703cb637efce6ef2cae890f8783",
50
+ "language": "Python",
51
+ "lines": 5,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 17713
55
+ },
56
+ {
57
+ "path": "binn/model/binn.py",
58
+ "sha256": "01cb16f4c7c63365d10afbf190e4a4bfac11ed5ee57168a4336adf56ad49c0fd",
59
+ "language": "Python",
60
+ "lines": 289,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 25421
64
+ },
65
+ {
66
+ "path": "binn/model/dataloader.py",
67
+ "sha256": "5db5b6f33dbc3a90294a6bca1a89e66f379eab7283f15aff2d832df7e3fda1e5",
68
+ "language": "Python",
69
+ "lines": 182,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 23948
73
+ },
74
+ {
75
+ "path": "binn/model/pathway_network.py",
76
+ "sha256": "c94fe02be6047b59fdecbd21f9882fa784608e2e36a7c2b2b98bc10425d28aa5",
77
+ "language": "Python",
78
+ "lines": 322,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 25922
82
+ },
83
+ {
84
+ "path": "binn/model/trainer.py",
85
+ "sha256": "05c8b1f053d797552d91e52b2ef1afa10fc33807297abccf5e842554fb36e888",
86
+ "language": "Python",
87
+ "lines": 156,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 23099
91
+ },
92
+ {
93
+ "path": "binn/model/util.py",
94
+ "sha256": "48227a997141332f1085cb32fe8f999d86f1cdb87d4b2d28e94ef333415a4b07",
95
+ "language": "Python",
96
+ "lines": 37,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 19157
100
+ },
101
+ {
102
+ "path": "binn/plot/network.py",
103
+ "sha256": "fc42ffde09671d0aa1e3d0343337b4b3e4fceb885e80fc083ba1d8074c420505",
104
+ "language": "Python",
105
+ "lines": 339,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 26083
109
+ },
110
+ {
111
+ "path": "binn/plot/util.py",
112
+ "sha256": "d1599c2d7c6ab6da7eda615e8841977d94af03d8f76fe7bcaee6f69f8b34ccd3",
113
+ "language": "Python",
114
+ "lines": 64,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 20861
118
+ },
119
+ {
120
+ "path": "colab/BINN_colab.ipynb",
121
+ "sha256": "b15b86f4df3b1f60c78f07bf125a9447d90d8294d181b9677e27ee61dc1ffe8f",
122
+ "language": "Jupyter",
123
+ "lines": 228,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 7489
127
+ },
128
+ {
129
+ "path": "docs/binn_example.ipynb",
130
+ "sha256": "c433d057910dd24776dbf72f1bfd321abc694645fceb8fee53e031bd2d321096",
131
+ "language": "Jupyter",
132
+ "lines": 120,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 7227
136
+ },
137
+ {
138
+ "path": "docs/robustness.ipynb",
139
+ "sha256": "d5eb781a9fdcbcd171319f8c17b9b9534c9bea18a3de0d550dcd4e7e5417219b",
140
+ "language": "Jupyter",
141
+ "lines": 84,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 7195
145
+ },
146
+ {
147
+ "path": "docs/shap_example.ipynb",
148
+ "sha256": "f631b1f2a4948446658cf0490b2fec0e7d6000e35cb24230129cf3c81d826167",
149
+ "language": "Jupyter",
150
+ "lines": 63,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 7093
154
+ },
155
+ {
156
+ "path": "setup.py",
157
+ "sha256": "aae7cdfd0ab2dcea97d91ea706c0031366d2d0fa77537df6913839a85c3a501f",
158
+ "language": "Python",
159
+ "lines": 24,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 18396
163
+ },
164
+ {
165
+ "path": "tests/test_binn.py",
166
+ "sha256": "c4153ab69cde16e2614749e63d247c91e5c277c3ad25034d5660e8752b69ded4",
167
+ "language": "Python",
168
+ "lines": 200,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 23714
172
+ },
173
+ {
174
+ "path": "tests/test_explainer.py",
175
+ "sha256": "09926fc47c977383963d68f0082f6e62dc3f58c1d70e4c9abd744b1567a53911",
176
+ "language": "Python",
177
+ "lines": 189,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 24021
181
+ },
182
+ {
183
+ "path": "tests/test_pathway_network.py",
184
+ "sha256": "1e8a36f76a1c54288710fdab382344f53db81d226d387898f81111e5c2c0c65c",
185
+ "language": "Python",
186
+ "lines": 240,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 25189
190
+ }
191
+ ]
192
+ }
manifests/fa/github.com__nicalab__graphycs.json ADDED
@@ -0,0 +1,138 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/nicalab/graphycs",
4
+ "url": "https://github.com/NICALab/GRAPHYCS",
5
+ "host": "github.com",
6
+ "commit": "84c2c588030f909abf4c6da899f65f40afb49a9f",
7
+ "license": "GPL-3.0",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "GRAPHYCS_demo.ipynb",
13
+ "sha256": "a97253fafcb2e3361492967184cd8ba6acc4f42ffdb1ae417446d5c4db711dad",
14
+ "language": "Jupyter",
15
+ "lines": 408,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 7666
19
+ },
20
+ {
21
+ "path": "LICENSE",
22
+ "sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986",
23
+ "language": "License",
24
+ "lines": 674,
25
+ "truncated": false,
26
+ "block": 1,
27
+ "row": 2235
28
+ },
29
+ {
30
+ "path": "README.md",
31
+ "sha256": "288fc998e0553ddeab3fea40b5a531e8222fac6145f1f1affed7641a254b004c",
32
+ "language": "Text",
33
+ "lines": 181,
34
+ "truncated": false,
35
+ "block": 4,
36
+ "row": 2624
37
+ },
38
+ {
39
+ "path": "graphycs/GRAPHYCS_spatially_invariant_lsm.py",
40
+ "sha256": "339c7f90169d8f7445885663317ecfe992e4e04898f1ccd2b495677fd6c36e25",
41
+ "language": "Python",
42
+ "lines": 434,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 26916
46
+ },
47
+ {
48
+ "path": "graphycs/GRAPHYCS_spatially_invariant_wf.py",
49
+ "sha256": "f65e773371036d387148681721e18fab7dc33201ad9a15e2da102f744263b5ac",
50
+ "language": "Python",
51
+ "lines": 396,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 26676
55
+ },
56
+ {
57
+ "path": "graphycs/GRAPHYCS_spatially_variant_lsm.py",
58
+ "sha256": "9aa2ac798cb999ad94f8c14a57b49e1eff7af04b00d6d6dac5edc19df1009649",
59
+ "language": "Python",
60
+ "lines": 433,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 27022
64
+ },
65
+ {
66
+ "path": "graphycs/GRAPHYCS_spatially_variant_wf.py",
67
+ "sha256": "cc37ca65281e5337b36454896f05263e5829be7682b2415d31455a90fadd781e",
68
+ "language": "Python",
69
+ "lines": 410,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 26890
73
+ },
74
+ {
75
+ "path": "graphycs/dset.py",
76
+ "sha256": "28e14ba8203aad41737cf976b70a7f07da5477cd723c47faced72813271bd82d",
77
+ "language": "Python",
78
+ "lines": 34,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 19258
82
+ },
83
+ {
84
+ "path": "graphycs/forward_model_lsm.py",
85
+ "sha256": "2bb5ff678ad2300817853a65f7b68e4017059e71b407f691421f65c89fa3a355",
86
+ "language": "Python",
87
+ "lines": 173,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 24447
91
+ },
92
+ {
93
+ "path": "graphycs/forward_model_lsm_variant.py",
94
+ "sha256": "1f8c539c3386226d0c9c1294c45641ff873d80095482db6adf2c16b34528a49c",
95
+ "language": "Python",
96
+ "lines": 203,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 25238
100
+ },
101
+ {
102
+ "path": "graphycs/forward_model_wf.py",
103
+ "sha256": "aae838e08303f0bbe67797840b66e031ed05c09a40ce1097c94d28dcc6c30994",
104
+ "language": "Python",
105
+ "lines": 151,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 23958
109
+ },
110
+ {
111
+ "path": "graphycs/forward_model_wf_variant.py",
112
+ "sha256": "1374828938eac04f42a7c9e65c78314be3b67a8a5c32889e7b9bf9a69071e3ac",
113
+ "language": "Python",
114
+ "lines": 179,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 24789
118
+ },
119
+ {
120
+ "path": "graphycs/self_calibration.py",
121
+ "sha256": "4b49295eabbc484b98f132dc97ce08cee08facf989e1b5d00c9210339bac33a3",
122
+ "language": "Python",
123
+ "lines": 210,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 24815
127
+ },
128
+ {
129
+ "path": "graphycs/utils.py",
130
+ "sha256": "cae3ca9c87147643bbf0eef321378b9b2ea79c9a791be10e7b61727a01228c8f",
131
+ "language": "Python",
132
+ "lines": 300,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 25472
136
+ }
137
+ ]
138
+ }
manifests/fa/github.com__shekharlab__amacrinecells.json ADDED
@@ -0,0 +1,246 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/shekharlab/amacrinecells",
4
+ "url": "https://github.com/shekharlab/AmacrineCells",
5
+ "host": "github.com",
6
+ "commit": "560dae2585e4d5a6115e5f1a7e03f5add2ae4133",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "1fd68528c897104167ddf081d97af36ab5f3a01cd6a9b2a73b1b9be80888a81c",
14
+ "language": "License",
15
+ "lines": 21,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 7955
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "102b5772fd20a4bb094784d60b7ad0aefd80c1d88f1e56f50c1056fa034bb810",
23
+ "language": "Text",
24
+ "lines": 45,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2401
28
+ },
29
+ {
30
+ "path": "src/0_run.R",
31
+ "sha256": "cc42bacadd139c6e4f2972bea194845506ad0cb3309b56beaf2d8f3bb0f223ab",
32
+ "language": "R",
33
+ "lines": 385,
34
+ "truncated": false,
35
+ "block": 4,
36
+ "row": 1085
37
+ },
38
+ {
39
+ "path": "src/1_species_clustering.Rmd",
40
+ "sha256": "4913941762b46f1dcb47af7069327200b221a62124db0f5baa7542a2b766833b",
41
+ "language": "R",
42
+ "lines": 968,
43
+ "truncated": false,
44
+ "block": 4,
45
+ "row": 1177
46
+ },
47
+ {
48
+ "path": "src/2_orthotype_analysis.Rmd",
49
+ "sha256": "13571b119efb76b18d570feae80a0679f7ddf5ef82c928037977b30fed231b8f",
50
+ "language": "R",
51
+ "lines": 4859,
52
+ "truncated": true,
53
+ "block": 4,
54
+ "row": 1248
55
+ },
56
+ {
57
+ "path": "src/3_literature_proportions.Rmd",
58
+ "sha256": "4dab2eee27f3cb0eadc63120e00ddb43a27c846b2970b87311b879d38b9a5977",
59
+ "language": "R",
60
+ "lines": 236,
61
+ "truncated": false,
62
+ "block": 4,
63
+ "row": 846
64
+ },
65
+ {
66
+ "path": "src/4_cluster_reproducibility.Rmd",
67
+ "sha256": "d715b10681059a1e0328113f4fdf2bd223434054665ff6bd33d0d70a161be140",
68
+ "language": "R",
69
+ "lines": 677,
70
+ "truncated": false,
71
+ "block": 4,
72
+ "row": 1130
73
+ },
74
+ {
75
+ "path": "src/5_tf_analysis.Rmd",
76
+ "sha256": "7df54d7e830e95fa45bedb774a6f807c8157c9f9decbe70e3abe71ee7c7dd599",
77
+ "language": "R",
78
+ "lines": 2138,
79
+ "truncated": false,
80
+ "block": 4,
81
+ "row": 1232
82
+ },
83
+ {
84
+ "path": "src/6_samap_analysis.ipynb",
85
+ "sha256": "b61bdcbc694073735af6b2241d2f6755e49041febfc10932ae39dc6a91a3a008",
86
+ "language": "Jupyter",
87
+ "lines": 655,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 7796
91
+ },
92
+ {
93
+ "path": "src/7_sac_analysis.Rmd",
94
+ "sha256": "14004ec269befc3c6f1b294640f20f4b06d226d2e0ce0018536112409ce3a6e7",
95
+ "language": "R",
96
+ "lines": 1375,
97
+ "truncated": false,
98
+ "block": 4,
99
+ "row": 1213
100
+ },
101
+ {
102
+ "path": "src/8_figures.Rmd",
103
+ "sha256": "a4989b2bce7c34cfc30e5fef6ce0ff6f68976e9f6dc96b3727dbe0b4555b7204",
104
+ "language": "R",
105
+ "lines": 4412,
106
+ "truncated": true,
107
+ "block": 4,
108
+ "row": 1249
109
+ },
110
+ {
111
+ "path": "src/utils/DarioFunctions.py",
112
+ "sha256": "325e27d54f88cb082708a225eb4d69ccb7f9d5a45b225923132708defcccbd78",
113
+ "language": "Python",
114
+ "lines": 1027,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 27820
118
+ },
119
+ {
120
+ "path": "src/utils/KS_fxns.R",
121
+ "sha256": "6781470ba6812a2ed9eead0a6230e1ba74c2bf75a0c7e1d1d671ff05bde35e2f",
122
+ "language": "R",
123
+ "lines": 552,
124
+ "truncated": false,
125
+ "block": 4,
126
+ "row": 1057
127
+ },
128
+ {
129
+ "path": "src/utils/MappingExample.R",
130
+ "sha256": "5cad5453f0aeb0b164f73c1b7a33900438b46ff84de68363b74d391814302339",
131
+ "language": "R",
132
+ "lines": 37,
133
+ "truncated": false,
134
+ "block": 4,
135
+ "row": 328
136
+ },
137
+ {
138
+ "path": "src/utils/SamapFunctions.py",
139
+ "sha256": "81f24ec2829824a032a5817ea3d4507bbe2a02c010d8de5631cf912956e21bf9",
140
+ "language": "Python",
141
+ "lines": 1034,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 27826
145
+ },
146
+ {
147
+ "path": "src/utils/SmartMatrix.R",
148
+ "sha256": "905aad9de86810b598a702b7bdd428e98abaf54676f46058d25d784dce336423",
149
+ "language": "R",
150
+ "lines": 149,
151
+ "truncated": false,
152
+ "block": 4,
153
+ "row": 588
154
+ },
155
+ {
156
+ "path": "src/utils/dario_functions.R",
157
+ "sha256": "847c12156e8a507ab3d361da5ab0041a7d9e65d93c0cff33c3fb20fb55fdf85d",
158
+ "language": "R",
159
+ "lines": 5677,
160
+ "truncated": true,
161
+ "block": 4,
162
+ "row": 1252
163
+ },
164
+ {
165
+ "path": "src/utils/documented-functions.R/clustering.R",
166
+ "sha256": "e04f7c54c2e2bccf196da7f93bb305a634ff3d76978a0087c5a89e4a2543dbe6",
167
+ "language": "R",
168
+ "lines": 193,
169
+ "truncated": false,
170
+ "block": 4,
171
+ "row": 886
172
+ },
173
+ {
174
+ "path": "src/utils/objects.R",
175
+ "sha256": "9fbe3e50e8d4c8b8ee512e8405e1f8c7d20e2e3febb401fa30119ea625388b3e",
176
+ "language": "R",
177
+ "lines": 1187,
178
+ "truncated": false,
179
+ "block": 4,
180
+ "row": 1197
181
+ },
182
+ {
183
+ "path": "src/utils/plotCellTypePhylo.R",
184
+ "sha256": "3e9699eab421bc13f80c9fe84787132157ae8db14f633086ae09f56cc5620416",
185
+ "language": "R",
186
+ "lines": 580,
187
+ "truncated": false,
188
+ "block": 4,
189
+ "row": 1088
190
+ },
191
+ {
192
+ "path": "src/utils/plottingFxns.R",
193
+ "sha256": "ab835cfbc55c9a40da3280db632f8ae331bfece4434ede8f9eefad80570b5877",
194
+ "language": "R",
195
+ "lines": 581,
196
+ "truncated": false,
197
+ "block": 4,
198
+ "row": 1107
199
+ },
200
+ {
201
+ "path": "src/utils/rename.sh",
202
+ "sha256": "de00502862ec9493e48663361f07063b99df97f4e5dd33963fcfc63f93dd021f",
203
+ "language": "Shell",
204
+ "lines": 27,
205
+ "truncated": false,
206
+ "block": 4,
207
+ "row": 1572
208
+ },
209
+ {
210
+ "path": "src/utils/utilFxns.R",
211
+ "sha256": "e5a58bdd6a509a54ee3b35a0cb7fc20723aaa421de61f12aaf38a5d8571928a6",
212
+ "language": "R",
213
+ "lines": 457,
214
+ "truncated": false,
215
+ "block": 4,
216
+ "row": 1063
217
+ },
218
+ {
219
+ "path": "src/utils/wrappers.R",
220
+ "sha256": "4bf8d06989ea050f9f0187c878cbbec1456a449ed522407d6788df0af7c3b392",
221
+ "language": "R",
222
+ "lines": 3949,
223
+ "truncated": false,
224
+ "block": 4,
225
+ "row": 1247
226
+ },
227
+ {
228
+ "path": "src/utils/xgboost_train.R",
229
+ "sha256": "223e997ee705def41d17f9ad95f112b97618faf1fbfb01e39aa9db32054ed60f",
230
+ "language": "R",
231
+ "lines": 238,
232
+ "truncated": false,
233
+ "block": 4,
234
+ "row": 889
235
+ },
236
+ {
237
+ "path": "src/utils/xgboost_train_DT.R",
238
+ "sha256": "ac5066fc8c415924cc9546aff1c29696b9e3931abc691630affebdf6e366f7e5",
239
+ "language": "R",
240
+ "lines": 393,
241
+ "truncated": false,
242
+ "block": 4,
243
+ "row": 1025
244
+ }
245
+ ]
246
+ }
manifests/fa/zenodo__18791231.json ADDED
@@ -0,0 +1,210 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:18791231",
4
+ "url": "http://dx.doi.org/10.5281/zenodo.18791231",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "CC-BY-4.0",
8
+ "license_confirmed_by": "license of the archive's record",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "CustomColormap.m",
13
+ "sha256": "10f78f4bda3d0b757d888330845de124848b73bcb718e466781db993a185ee9c",
14
+ "language": "MATLAB",
15
+ "lines": 195,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 14908
19
+ },
20
+ {
21
+ "path": "G_EpochTS.m",
22
+ "sha256": "513d49e317af0ef1bac8ad9e052ae995193ad2be0beccbaf269547c5575c30d9",
23
+ "language": "MATLAB",
24
+ "lines": 162,
25
+ "truncated": false,
26
+ "block": 3,
27
+ "row": 14713
28
+ },
29
+ {
30
+ "path": "G_Imagesc.m",
31
+ "sha256": "9101fc99e15757ac59a5c752c35cd7bcd5d547668f45adb335f6e03010c1876f",
32
+ "language": "MATLAB",
33
+ "lines": 1763,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 17201
37
+ },
38
+ {
39
+ "path": "G_Outline_Pixels.m",
40
+ "sha256": "361c6aff84be13b528e408aa442e83078ea4566a331181b037f664b949ea5202",
41
+ "language": "MATLAB",
42
+ "lines": 293,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 16147
46
+ },
47
+ {
48
+ "path": "G_Outline_Range.m",
49
+ "sha256": "3c4acc68f221b97be94c7b935eb946b13c94bb31c4da8b955729d012bcacd806",
50
+ "language": "MATLAB",
51
+ "lines": 89,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 12639
55
+ },
56
+ {
57
+ "path": "G_PowChange_Clust.m",
58
+ "sha256": "a7195f0fbf461e7d3abb9f2229f1f1e72eb31ea4d926949a2ff973239e3f9076",
59
+ "language": "MATLAB",
60
+ "lines": 283,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 15988
64
+ },
65
+ {
66
+ "path": "G_RangeLoc.m",
67
+ "sha256": "eaa8b49637ce2f1415362caf80e14bda4c1f1da44039fe42f632d5a9c315ca81",
68
+ "language": "MATLAB",
69
+ "lines": 50,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 10410
73
+ },
74
+ {
75
+ "path": "G_Rescale.m",
76
+ "sha256": "32f7e39802323bcc73dea69cda60f937b16b06e08854271153acbdc05c692023",
77
+ "language": "MATLAB",
78
+ "lines": 103,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 13149
82
+ },
83
+ {
84
+ "path": "G_Smooth.m",
85
+ "sha256": "569b3b5f8473b311f0e4e350eee03359295e47e5bb168f532babb091be8eabf6",
86
+ "language": "MATLAB",
87
+ "lines": 129,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 13505
91
+ },
92
+ {
93
+ "path": "G_SparseArgs.m",
94
+ "sha256": "14ef436c6f4af5c7803ce1720589050c3ea6e2d68b0565585efd2a6156855946",
95
+ "language": "MATLAB",
96
+ "lines": 124,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 13392
100
+ },
101
+ {
102
+ "path": "G_fdr.m",
103
+ "sha256": "ebc5d90659cd2ddca25c1f2366d1b2aac862a1487cef9d9d35d5249d8f44dc76",
104
+ "language": "MATLAB",
105
+ "lines": 153,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 14159
109
+ },
110
+ {
111
+ "path": "G_p2z.m",
112
+ "sha256": "acc4383996fb81897adbc03fad1b9a07235766c8c4adceef875f10198cf3613a",
113
+ "language": "MATLAB",
114
+ "lines": 18,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 8673
118
+ },
119
+ {
120
+ "path": "PermutAmpChange_Commonbaseline.m",
121
+ "sha256": "30d87476fb4dedfa5f3397fbdde2ea1a551f745916a4289e84fe4a92c5241dc9",
122
+ "language": "MATLAB",
123
+ "lines": 253,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 15717
127
+ },
128
+ {
129
+ "path": "Script_Figure1plots.m",
130
+ "sha256": "2f8e85b05249c4a46dc2b53657df45f0d7c90457cf2ded8a1d93064a778a5236",
131
+ "language": "MATLAB",
132
+ "lines": 131,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 15148
136
+ },
137
+ {
138
+ "path": "code_fig1h.m",
139
+ "sha256": "6ea291a898455b3b90c934a1343b1c856c993e9a31ec10518a0bf69c55255ced",
140
+ "language": "MATLAB",
141
+ "lines": 44,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 11732
145
+ },
146
+ {
147
+ "path": "code_fig2_OdorImageCue.m",
148
+ "sha256": "0e7b9c340da016c325d4d0bb6bfbb5b2196accf9aeda6a4ccdf4ed8ebbab1ade",
149
+ "language": "MATLAB",
150
+ "lines": 394,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 16824
154
+ },
155
+ {
156
+ "path": "code_fig2a.m",
157
+ "sha256": "5a70cd04b3bd629be025a9a1b769233a749a9e5ec81b32ccf23ab4bbdb2ee9f9",
158
+ "language": "MATLAB",
159
+ "lines": 126,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 14990
163
+ },
164
+ {
165
+ "path": "code_fig3.m",
166
+ "sha256": "f228e76670468ed2d3659eed19ad4f1c47aa097a8d40ba87a5cfa21c86dcf5b0",
167
+ "language": "MATLAB",
168
+ "lines": 429,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 16808
172
+ },
173
+ {
174
+ "path": "code_fig4.m",
175
+ "sha256": "e746a6ce609be9a9ae8189429780da212136dccd851fdb76939d2d39b8312895",
176
+ "language": "MATLAB",
177
+ "lines": 838,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 17138
181
+ },
182
+ {
183
+ "path": "code_fig6.m",
184
+ "sha256": "6b2183893f04e8d761162a910991d87c3f0a6fb6de6b4df23f881d4a8e8a53ad",
185
+ "language": "MATLAB",
186
+ "lines": 598,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 17053
190
+ },
191
+ {
192
+ "path": "code_suppFigs.m",
193
+ "sha256": "728d47c4377fa47a3e58ce7158718e33e3590bf1d032cc9d86fa712e4f3ad632",
194
+ "language": "MATLAB",
195
+ "lines": 1002,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 17168
199
+ },
200
+ {
201
+ "path": "dataScript.m",
202
+ "sha256": "cc3a34864d4973e6d8d93a37669354f4a965e2b96e8578a2257504e8b5d53c62",
203
+ "language": "MATLAB",
204
+ "lines": 776,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 17199
208
+ }
209
+ ]
210
+ }
manifests/fb/github.com__bruce-ywj__ernie-rna.json ADDED
@@ -0,0 +1,165 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/bruce-ywj/ernie-rna",
4
+ "url": "https://github.com/Bruce-ywj/ERNIE-RNA",
5
+ "host": "github.com",
6
+ "commit": "43bc06de1088ed03ffd7de918ad4b2c2a3346a43",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "b7aa7b89bff7b3c4cca2f78dc0900f038a7253bcbea9b780eca30b2bc1610ffb",
14
+ "language": "License",
15
+ "lines": 21,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 7968
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "d2b2ca2f33c4d4d1dac63659cff494631732b7ec87ac07ad99a0826e55bfa603",
23
+ "language": "Text",
24
+ "lines": 214,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2665
28
+ },
29
+ {
30
+ "path": "extract_embedding.py",
31
+ "sha256": "a4ca12787a5a59554162a5b0d4ad8381266dc9d5f203177f800e344fcaba73b9",
32
+ "language": "Python",
33
+ "lines": 172,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 24470
37
+ },
38
+ {
39
+ "path": "predict_3d_clossness.py",
40
+ "sha256": "ef1f0080b906cfd5f9e0bddc00a0337e8626d991e824778557fddd61b97d4eb6",
41
+ "language": "Python",
42
+ "lines": 211,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 25544
46
+ },
47
+ {
48
+ "path": "predict_MRL.py",
49
+ "sha256": "0c0334cffd5024755fafebe0c6a8ff866f07a1796087f0e9fa498ad9f1bfb748",
50
+ "language": "Python",
51
+ "lines": 433,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 26657
55
+ },
56
+ {
57
+ "path": "predict_ss_rna.py",
58
+ "sha256": "159fa2188b830d86927acff3d534e0668d249eadf12af4bed32ba3f62f6508b8",
59
+ "language": "Python",
60
+ "lines": 321,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 26047
64
+ },
65
+ {
66
+ "path": "src/downstream_heads/closeness_model.py",
67
+ "sha256": "b29c6ad0a45641d5334c2af1557bcdc3d353a1baa053c658e77271b2b8c97e16",
68
+ "language": "Python",
69
+ "lines": 138,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 23563
73
+ },
74
+ {
75
+ "path": "src/ernie_rna/__init__.py",
76
+ "sha256": "fe58f190c85b09e016da56a6335ade7ab9a46bed68d4db43d038501036ce7269",
77
+ "language": "Python",
78
+ "lines": 3,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 17459
82
+ },
83
+ {
84
+ "path": "src/ernie_rna/criterions/__init__.py",
85
+ "sha256": "229fe5389dd4fe9a6e75e3d7a96bc7f940daf47939bdd39b71ef0028645def96",
86
+ "language": "Python",
87
+ "lines": 1,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 17413
91
+ },
92
+ {
93
+ "path": "src/ernie_rna/criterions/ernie_rna.py",
94
+ "sha256": "9fffe51a87880ebe45d6fbf9a1048384545b7ef98037da52d8a2274aaffdd655",
95
+ "language": "Python",
96
+ "lines": 229,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 24837
100
+ },
101
+ {
102
+ "path": "src/ernie_rna/models/__init__.py",
103
+ "sha256": "3c0e0bbd4be70ba686a6bcd2f5924849660104b059647ba468ef6d95848340f5",
104
+ "language": "Python",
105
+ "lines": 1,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 17389
109
+ },
110
+ {
111
+ "path": "src/ernie_rna/models/ernie_rna.py",
112
+ "sha256": "f82a9a934f539c97d4ea30145e3a5b8c6cc8b6f1fee8d6c1b3150aee26cab57c",
113
+ "language": "Python",
114
+ "lines": 1344,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 27980
118
+ },
119
+ {
120
+ "path": "src/ernie_rna/models/ernie_rna_utils.py",
121
+ "sha256": "1ccdd98bcec6d2c4c6bc6869168789449d01c8a3a61e81dba25a378242a5accb",
122
+ "language": "Python",
123
+ "lines": 348,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 26650
127
+ },
128
+ {
129
+ "path": "src/ernie_rna/models/prediction.py",
130
+ "sha256": "2833d2ed1ade79e8114cd0e538c8b8aa8e9a69db6600405856b5b299abfba817",
131
+ "language": "Python",
132
+ "lines": 258,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 24971
136
+ },
137
+ {
138
+ "path": "src/ernie_rna/tasks/__init__.py",
139
+ "sha256": "8594fb49819c56b69d4d7c24d1d608dd90b3f34167d70f1e4606497a339f0b5f",
140
+ "language": "Python",
141
+ "lines": 1,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 17359
145
+ },
146
+ {
147
+ "path": "src/ernie_rna/tasks/ernie_rna.py",
148
+ "sha256": "227a63ef1ac4caea5bfb3229af247424485c496e40697f5c4a862573b38a7af4",
149
+ "language": "Python",
150
+ "lines": 901,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 27761
154
+ },
155
+ {
156
+ "path": "src/utils.py",
157
+ "sha256": "6b19c8c352f82432c1aa1f47ba8ba75daf9128d629bdd3a103a1566b56ae0ab8",
158
+ "language": "Python",
159
+ "lines": 326,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 25947
163
+ }
164
+ ]
165
+ }
manifests/fb/github.com__kr-colab__popgen-npe.json ADDED
@@ -0,0 +1,588 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/kr-colab/popgen-npe",
4
+ "url": "https://github.com/kr-colab/popgen-npe",
5
+ "host": "github.com",
6
+ "commit": "e81dfe66d32ff194e42c3c68941e647f824e0a32",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "c0d9a42f0d310d5d2d411aa2eea8a3d60a6363816e0648ef6eb203b430d750ff",
14
+ "language": "License",
15
+ "lines": 21,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 7939
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "6b9a70985f88f3c899f9a7f092114280f80376484aa1ab466c2d95a51214e3dc",
23
+ "language": "Text",
24
+ "lines": 110,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2527
28
+ },
29
+ {
30
+ "path": "depr/amortized_dadi_workflow/scripts/dadi_simulators.py",
31
+ "sha256": "410ece5b0d97d32c2f672881ddc330c0e88e6d8285a0004e7667f18acb5a6e8a",
32
+ "language": "Python",
33
+ "lines": 184,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 24614
37
+ },
38
+ {
39
+ "path": "depr/amortized_dadi_workflow/scripts/plot_2d_comp_multinom.py",
40
+ "sha256": "a90e3a1b611cb96211b7aecf8686b9f25cd3382d0f98cbef82f25184e81c8c42",
41
+ "language": "Python",
42
+ "lines": 25,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 18720
46
+ },
47
+ {
48
+ "path": "depr/amortized_dadi_workflow/scripts/plot_confidence_intervals.py",
49
+ "sha256": "6f5a3f9e37f30ac57d64b691a3ed499b3d1a60cf30359d3d4a604774a2a8e505",
50
+ "language": "Python",
51
+ "lines": 36,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 19547
55
+ },
56
+ {
57
+ "path": "depr/amortized_dadi_workflow/scripts/plotting.py",
58
+ "sha256": "172665a5e1e4b575813b4653c96d2b8923c2b49bffda8af47c3bc45c83e5655c",
59
+ "language": "Python",
60
+ "lines": 49,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 19896
64
+ },
65
+ {
66
+ "path": "depr/amortized_dadi_workflow/scripts/posterior_ensemble.py",
67
+ "sha256": "a4197c7c5c026be4f92b255c066e1fde3a27e954739f9a0fe3bb24f624291603",
68
+ "language": "Python",
69
+ "lines": 22,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 18609
73
+ },
74
+ {
75
+ "path": "depr/amortized_dadi_workflow/scripts/simulate_default.py",
76
+ "sha256": "1cfdf195dfb28fd2d18526916923275847c67ddc2d9f50e3226d6edadab4d00f",
77
+ "language": "Python",
78
+ "lines": 17,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 18264
82
+ },
83
+ {
84
+ "path": "depr/amortized_dadi_workflow/scripts/simulate_from_posterior.py",
85
+ "sha256": "7c0ce484e1babee053d9a102c1d4bd8b4b69dae6e52242b284a6c49b1e4be77a",
86
+ "language": "Python",
87
+ "lines": 22,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 18715
91
+ },
92
+ {
93
+ "path": "depr/amortized_dadi_workflow/scripts/simulate_fs.py",
94
+ "sha256": "5f2a31195f51e2195f60cc9893a887beb81f08b563b47b9f753715e90d57c745",
95
+ "language": "Python",
96
+ "lines": 28,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 18582
100
+ },
101
+ {
102
+ "path": "depr/amortized_dadi_workflow/scripts/train_npe.py",
103
+ "sha256": "d1a5c239ba7bd3daa307b4f6063b575f92ed9d0956ad17817feec98dcab57f4a",
104
+ "language": "Python",
105
+ "lines": 88,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 21292
109
+ },
110
+ {
111
+ "path": "depr/plots/AraTha/compare_to_dadi_2epoch_model.ipynb",
112
+ "sha256": "67e704afab69d3d1aaad9c2eec36b62ccdb00d621d531a8fa1704d27a0ed68f2",
113
+ "language": "Jupyter",
114
+ "lines": 238,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 7572
118
+ },
119
+ {
120
+ "path": "docs/conf.py",
121
+ "sha256": "780409796549b7fe06d09214381475130d8522502301fd7f904c41aaa02d813c",
122
+ "language": "Python",
123
+ "lines": 55,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 19206
127
+ },
128
+ {
129
+ "path": "experiments/aratha-2epoch-extra/abc_utils.py",
130
+ "sha256": "b7d8aef0369a7058673212a06d41f672f8da7b0bb973f8f6f0bfe773d0123c14",
131
+ "language": "Python",
132
+ "lines": 334,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 25415
136
+ },
137
+ {
138
+ "path": "experiments/aratha-2epoch-extra/compare-posteriors.py",
139
+ "sha256": "ab8fd705f73f37b8820accc322ca3f25f19328c6b0b742c9e6f502413b2ccf67",
140
+ "language": "Python",
141
+ "lines": 738,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 27358
145
+ },
146
+ {
147
+ "path": "experiments/aratha-2epoch-extra/experiment.sh",
148
+ "sha256": "618cd5855b720636ba3a9031e87a4836f2be32ab9b340b226d577fce016c4528",
149
+ "language": "Shell",
150
+ "lines": 13,
151
+ "truncated": false,
152
+ "block": 4,
153
+ "row": 1425
154
+ },
155
+ {
156
+ "path": "experiments/aratha-2epoch-extra/plot-posterior-surfaces.py",
157
+ "sha256": "fcc7f05319be0c824ad3b61a8f0a28c4799b99af1ddc7c3148eaac4f3b3a8fb6",
158
+ "language": "Python",
159
+ "lines": 73,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 20822
163
+ },
164
+ {
165
+ "path": "experiments/aratha-2epoch/abc_utils.py",
166
+ "sha256": "b7d8aef0369a7058673212a06d41f672f8da7b0bb973f8f6f0bfe773d0123c14",
167
+ "language": "Python",
168
+ "lines": 334,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 25415
172
+ },
173
+ {
174
+ "path": "experiments/aratha-2epoch/compare-posteriors.py",
175
+ "sha256": "f38b9d27e983d2037c9e16810aef19fad854382fafe50857a74b7d5033f1a104",
176
+ "language": "Python",
177
+ "lines": 727,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 27333
181
+ },
182
+ {
183
+ "path": "experiments/aratha-2epoch/experiment.sh",
184
+ "sha256": "89e46a5905842f37c0a0a363a6222d4caff162fba1b238118cc23b83a89a8a96",
185
+ "language": "Shell",
186
+ "lines": 13,
187
+ "truncated": false,
188
+ "block": 4,
189
+ "row": 1417
190
+ },
191
+ {
192
+ "path": "experiments/aratha-2epoch/plot-posterior-surfaces.py",
193
+ "sha256": "fcc7f05319be0c824ad3b61a8f0a28c4799b99af1ddc7c3148eaac4f3b3a8fb6",
194
+ "language": "Python",
195
+ "lines": 73,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 20822
199
+ },
200
+ {
201
+ "path": "experiments/dependent-variable-popn-size/compare-analysis.py",
202
+ "sha256": "05d7e3a55923eced834ab61a169e87ab8f40c5c8a5a0b49f77b15834f0327224",
203
+ "language": "Python",
204
+ "lines": 264,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 24658
208
+ },
209
+ {
210
+ "path": "experiments/dependent-variable-popn-size/compare-posteriors.py",
211
+ "sha256": "dd922ba8d2ebe119c566f2b9794f43db1acd0c68b356da38edf8ab71fdb6e958",
212
+ "language": "Python",
213
+ "lines": 638,
214
+ "truncated": false,
215
+ "block": 3,
216
+ "row": 27155
217
+ },
218
+ {
219
+ "path": "experiments/dependent-variable-popn-size/plot-6-scenarios.py",
220
+ "sha256": "bd1267d3a3dfee5a8585655b2a98e88ff0409f522d3c194cb2096e2137b45e07",
221
+ "language": "Python",
222
+ "lines": 189,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 23841
226
+ },
227
+ {
228
+ "path": "experiments/dependent-variable-popn-size/run-ne-comparison-six-scenarios.sh",
229
+ "sha256": "1ca973827bcd10aacd3bc3fab6e706c0aa2c45234ba6b8a24568e74657ea5620",
230
+ "language": "Shell",
231
+ "lines": 130,
232
+ "truncated": false,
233
+ "block": 4,
234
+ "row": 2160
235
+ },
236
+ {
237
+ "path": "experiments/dependent-variable-popn-size/simulate-examples.sh",
238
+ "sha256": "0f76605744f84503aee057cc04bc6b9b30c5aa270c1906604d763119420d50a2",
239
+ "language": "Shell",
240
+ "lines": 33,
241
+ "truncated": false,
242
+ "block": 4,
243
+ "row": 1881
244
+ },
245
+ {
246
+ "path": "experiments/dependent-variable-popn-size/simulate-for-posterior.py",
247
+ "sha256": "fde2a2dc22c2325f830c5e8bdd1fe9bf37945e84128201cfdfd65f5d3bb3ee38",
248
+ "language": "Python",
249
+ "lines": 224,
250
+ "truncated": false,
251
+ "block": 3,
252
+ "row": 24148
253
+ },
254
+ {
255
+ "path": "experiments/dmel-isolation/experiment.sh",
256
+ "sha256": "abe4100e58dd93a494635598650f5bec758691996fca7dde1e91f6252e8344b0",
257
+ "language": "Shell",
258
+ "lines": 17,
259
+ "truncated": false,
260
+ "block": 4,
261
+ "row": 1460
262
+ },
263
+ {
264
+ "path": "experiments/dmel-isolation/package-data.sh",
265
+ "sha256": "d329013d425aefd1eafa06974f7151a6f2243bc4b1f7f88e73bdf7b3b0501dfd",
266
+ "language": "Shell",
267
+ "lines": 114,
268
+ "truncated": false,
269
+ "block": 4,
270
+ "row": 2114
271
+ },
272
+ {
273
+ "path": "experiments/dmel-isolation/plot-joint-posteriors.py",
274
+ "sha256": "c47b97be4e7ce6c67729b83f68c0a2dcbd7b3d0e37e03f68a4437611f3727771",
275
+ "language": "Python",
276
+ "lines": 342,
277
+ "truncated": false,
278
+ "block": 3,
279
+ "row": 26080
280
+ },
281
+ {
282
+ "path": "experiments/dmel-isolation/plot-rescaled-posteriors.py",
283
+ "sha256": "626fe0a542908af1ad5d49ad09052d5bcad68a2d6f48dbebf2d3fcffd9ea15d8",
284
+ "language": "Python",
285
+ "lines": 224,
286
+ "truncated": false,
287
+ "block": 3,
288
+ "row": 24473
289
+ },
290
+ {
291
+ "path": "experiments/dmel-isolation/plot-summary-stats.py",
292
+ "sha256": "5593e4f0a6cd910ecadd23083419ee6769dc909c1470b03104c128e217f27e25",
293
+ "language": "Python",
294
+ "lines": 230,
295
+ "truncated": false,
296
+ "block": 3,
297
+ "row": 24637
298
+ },
299
+ {
300
+ "path": "experiments/relernn-prior/experiment.sh",
301
+ "sha256": "5da4b2bd9982ee8d883b756fed63530c87a10c5d792563ab91b582d3a3a270de",
302
+ "language": "Shell",
303
+ "lines": 17,
304
+ "truncated": false,
305
+ "block": 4,
306
+ "row": 1447
307
+ },
308
+ {
309
+ "path": "experiments/relernn-prior/plot_coverage_comparison.py",
310
+ "sha256": "09dec6a08d0a3f238f4961b2cede8f3797377ae377eaf97c90cd381ff9daea6e",
311
+ "language": "Python",
312
+ "lines": 111,
313
+ "truncated": false,
314
+ "block": 3,
315
+ "row": 22372
316
+ },
317
+ {
318
+ "path": "experiments/relernn-prior/predict_on_true.py",
319
+ "sha256": "a6187d5ccbc8e70df0f43c2124d0e625dc91a8ca77aeeeeb99797a0e29d3e427",
320
+ "language": "Python",
321
+ "lines": 204,
322
+ "truncated": false,
323
+ "block": 3,
324
+ "row": 24207
325
+ },
326
+ {
327
+ "path": "experiments/variable-popn-size/baselines/msmc2_utils.py",
328
+ "sha256": "45655332b3789f36b4b14071eb837fca696811bfefcb7c15b977b41ff3b5f50c",
329
+ "language": "Python",
330
+ "lines": 351,
331
+ "truncated": false,
332
+ "block": 3,
333
+ "row": 25548
334
+ },
335
+ {
336
+ "path": "experiments/variable-popn-size/baselines/run_baselines.py",
337
+ "sha256": "09be7194c3a3ff02cca9f6a3003f594362d8e6e8f90ec1210909fcfefb8c8424",
338
+ "language": "Python",
339
+ "lines": 112,
340
+ "truncated": false,
341
+ "block": 3,
342
+ "row": 21776
343
+ },
344
+ {
345
+ "path": "experiments/variable-popn-size/compare-analysis.py",
346
+ "sha256": "8d9f5c2372f758c93f295f62a9f1deb3287845301ddafb54ba8b15942ccafc34",
347
+ "language": "Python",
348
+ "lines": 253,
349
+ "truncated": false,
350
+ "block": 3,
351
+ "row": 24431
352
+ },
353
+ {
354
+ "path": "experiments/variable-popn-size/compare-posteriors.py",
355
+ "sha256": "1f0b79ee2f2c6f4aede2e71b3a750381e9e6cf40185ef6a2a84acf845ce0fc31",
356
+ "language": "Python",
357
+ "lines": 617,
358
+ "truncated": false,
359
+ "block": 3,
360
+ "row": 27088
361
+ },
362
+ {
363
+ "path": "experiments/variable-popn-size/create-3x3-panel-with-baselines.py",
364
+ "sha256": "947935e567ba14bb29db9f04ee03615491ea94d9c4085134aa9f22123487dbaa",
365
+ "language": "Python",
366
+ "lines": 200,
367
+ "truncated": false,
368
+ "block": 3,
369
+ "row": 24199
370
+ },
371
+ {
372
+ "path": "experiments/variable-popn-size/create-3x3-panel.py",
373
+ "sha256": "135e551f2aed25cb8c067edcda9cff801a35a024a2a5a9fb960fe2d499d3e069",
374
+ "language": "Python",
375
+ "lines": 189,
376
+ "truncated": false,
377
+ "block": 3,
378
+ "row": 23840
379
+ },
380
+ {
381
+ "path": "experiments/variable-popn-size/run-ne-comparison-three-scenarios.sh",
382
+ "sha256": "b91c197217bba0dba22ef76818c3b186c29aa2b8f54e41f74202ad673d42d470",
383
+ "language": "Shell",
384
+ "lines": 86,
385
+ "truncated": false,
386
+ "block": 4,
387
+ "row": 2095
388
+ },
389
+ {
390
+ "path": "experiments/variable-popn-size/simulate-examples.sh",
391
+ "sha256": "693a3d92bc0427a6cf2fe6aeeadbb6509b737d387deebc734def8311ffc25d61",
392
+ "language": "Shell",
393
+ "lines": 61,
394
+ "truncated": false,
395
+ "block": 4,
396
+ "row": 1983
397
+ },
398
+ {
399
+ "path": "experiments/variable-popn-size/simulate-for-posterior.py",
400
+ "sha256": "1b37543fb33292a40456bb70f9862f73f2e5fc7d23b361b0b12cfb9f4fa4b599",
401
+ "language": "Python",
402
+ "lines": 370,
403
+ "truncated": false,
404
+ "block": 3,
405
+ "row": 25792
406
+ },
407
+ {
408
+ "path": "resources/util/simulate-vcf.py",
409
+ "sha256": "38949d0709358516f0e13494a072ec78ee794758ab0bb49d0a1ea27294c059bf",
410
+ "language": "Python",
411
+ "lines": 141,
412
+ "truncated": false,
413
+ "block": 3,
414
+ "row": 22354
415
+ },
416
+ {
417
+ "path": "tests/test_polarise.py",
418
+ "sha256": "9f856c8f38471deb16ea543bd51eadbb54f7a221d76f421d5d55817d0e1fd866",
419
+ "language": "Python",
420
+ "lines": 110,
421
+ "truncated": false,
422
+ "block": 3,
423
+ "row": 22115
424
+ },
425
+ {
426
+ "path": "tests/test_workflow_script.py",
427
+ "sha256": "017e0f3ca34f4e9e47766d03a778d846488a4b2b7503ccd10c9386a46dea6c71",
428
+ "language": "Python",
429
+ "lines": 381,
430
+ "truncated": false,
431
+ "block": 3,
432
+ "row": 25659
433
+ },
434
+ {
435
+ "path": "workflow/scripts/data_handlers.py",
436
+ "sha256": "2a49733e3223be9240dc14a570fa5834bcbbf90deab6924e255e1513ea5e76a2",
437
+ "language": "Python",
438
+ "lines": 156,
439
+ "truncated": false,
440
+ "block": 3,
441
+ "row": 23120
442
+ },
443
+ {
444
+ "path": "workflow/scripts/embedding_networks.py",
445
+ "sha256": "239b35097ac93dea27dfd4be4af364474c86b3f8229d2a05ed3a8da761e3a1b2",
446
+ "language": "Python",
447
+ "lines": 397,
448
+ "truncated": false,
449
+ "block": 3,
450
+ "row": 26548
451
+ },
452
+ {
453
+ "path": "workflow/scripts/infer_batch.py",
454
+ "sha256": "9c19507d206b3c27e064c39abfc597722a12e5e837c90c4823fea22a99b2d2de",
455
+ "language": "Python",
456
+ "lines": 60,
457
+ "truncated": false,
458
+ "block": 3,
459
+ "row": 20426
460
+ },
461
+ {
462
+ "path": "workflow/scripts/plot_diagnostics.py",
463
+ "sha256": "22ccc323dc8da9a6395ee4eda05fb98bbe393714e2ee48b3ff08ccbd60c4c316",
464
+ "language": "Python",
465
+ "lines": 230,
466
+ "truncated": false,
467
+ "block": 3,
468
+ "row": 24717
469
+ },
470
+ {
471
+ "path": "workflow/scripts/plot_simulation_stats.py",
472
+ "sha256": "315ba0fadcd9c175a17cad5cd38e81dee2f4a08489fb84cbfb0c51e0abcefca3",
473
+ "language": "Python",
474
+ "lines": 105,
475
+ "truncated": false,
476
+ "block": 3,
477
+ "row": 21906
478
+ },
479
+ {
480
+ "path": "workflow/scripts/plot_tree_stats.py",
481
+ "sha256": "7a5c4287bb68328aeea310915e2ee4c7c57c0d37c80fcdcfa7786e49a2ed3ed4",
482
+ "language": "Python",
483
+ "lines": 84,
484
+ "truncated": false,
485
+ "block": 3,
486
+ "row": 20945
487
+ },
488
+ {
489
+ "path": "workflow/scripts/predict_windows.py",
490
+ "sha256": "e92038d7c27d7397858f1861973dc9b061d8ac6e39ad40d47990eb54ba479ce7",
491
+ "language": "Python",
492
+ "lines": 141,
493
+ "truncated": false,
494
+ "block": 3,
495
+ "row": 22771
496
+ },
497
+ {
498
+ "path": "workflow/scripts/process_batch.py",
499
+ "sha256": "27b2f870f0fb33a6266fcda52bcf6944d6d7c5bb5995a19f1cab85a407019db2",
500
+ "language": "Python",
501
+ "lines": 27,
502
+ "truncated": false,
503
+ "block": 3,
504
+ "row": 18708
505
+ },
506
+ {
507
+ "path": "workflow/scripts/setup_prediction.py",
508
+ "sha256": "252e8c333bcc3f5e944bce4fb41e98b27546861c5f7580cc0397cb9fb2c9cdc1",
509
+ "language": "Python",
510
+ "lines": 156,
511
+ "truncated": false,
512
+ "block": 3,
513
+ "row": 23954
514
+ },
515
+ {
516
+ "path": "workflow/scripts/setup_training.py",
517
+ "sha256": "e1893e915314eb68f2d0d35f7a035cd58324a0cec0d2255932883015bc8be9ea",
518
+ "language": "Python",
519
+ "lines": 54,
520
+ "truncated": false,
521
+ "block": 3,
522
+ "row": 20000
523
+ },
524
+ {
525
+ "path": "workflow/scripts/simulate_batch.py",
526
+ "sha256": "7f5a3a3787983eb4d23144559d6618a169d3d6fa75228cacbae2888d9cc5e0fd",
527
+ "language": "Python",
528
+ "lines": 32,
529
+ "truncated": false,
530
+ "block": 3,
531
+ "row": 18866
532
+ },
533
+ {
534
+ "path": "workflow/scripts/train_embedding_network.py",
535
+ "sha256": "f57ce00691eef9d35819d15a32679248d0920627fa96bd12256e1ffd93d2b7e8",
536
+ "language": "Python",
537
+ "lines": 190,
538
+ "truncated": false,
539
+ "block": 3,
540
+ "row": 23772
541
+ },
542
+ {
543
+ "path": "workflow/scripts/train_npe_on_embeddings.py",
544
+ "sha256": "d23707ba6265549d620de278babdf5d17a39af8fa1aaadbf1642a63a65206f08",
545
+ "language": "Python",
546
+ "lines": 143,
547
+ "truncated": false,
548
+ "block": 3,
549
+ "row": 22640
550
+ },
551
+ {
552
+ "path": "workflow/scripts/train_npe_on_features.py",
553
+ "sha256": "d0b4179b7270c39a65fa3eb4d8eba5bd9d46f134a7b6a0d2afb7eb580c0d213c",
554
+ "language": "Python",
555
+ "lines": 142,
556
+ "truncated": false,
557
+ "block": 3,
558
+ "row": 22850
559
+ },
560
+ {
561
+ "path": "workflow/scripts/ts_processors.py",
562
+ "sha256": "b94092522becf1eacb41f54b3dd8ec3eb469a6ceaf0b21561cbf7322ee682195",
563
+ "language": "Python",
564
+ "lines": 462,
565
+ "truncated": false,
566
+ "block": 3,
567
+ "row": 26774
568
+ },
569
+ {
570
+ "path": "workflow/scripts/ts_simulators.py",
571
+ "sha256": "752a052ccca782a705a1de47fac4cbc7fe86535904100bc07e0b253e653034e7",
572
+ "language": "Python",
573
+ "lines": 519,
574
+ "truncated": false,
575
+ "block": 3,
576
+ "row": 27079
577
+ },
578
+ {
579
+ "path": "workflow/scripts/utils.py",
580
+ "sha256": "8dd425d7a237f9afe37c08e549e33e0fadc6a67bc4fbf0817f85ca8839411346",
581
+ "language": "Python",
582
+ "lines": 53,
583
+ "truncated": false,
584
+ "block": 3,
585
+ "row": 19758
586
+ }
587
+ ]
588
+ }
manifests/fc/github.com__mmtrebuchet__bpreveal.json ADDED
@@ -0,0 +1,732 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/mmtrebuchet/bpreveal",
4
+ "url": "https://github.com/mmtrebuchet/bpreveal",
5
+ "host": "github.com",
6
+ "commit": "2611b30a39a8eed29b8f3f8821bf50028db9fa4d",
7
+ "license": "GPL-3.0",
8
+ "license_confirmed_by": "license file COPYING",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "COPYING",
13
+ "sha256": "5fe652093e1b63e57f523bbbdba5d1921170b0ffe41edd798f3ae36cb0434f01",
14
+ "language": "License",
15
+ "lines": 633,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8168
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "a49cbb6278863e49e6410b28faf6bb00c773afda102112567b551be5af5dfe27",
23
+ "language": "Text",
24
+ "lines": 82,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2516
28
+ },
29
+ {
30
+ "path": "doc/build.py",
31
+ "sha256": "078a6f072b4d8992c7e242f19ee6559eb5324735e483f2abccddfb419d751c1a",
32
+ "language": "Python",
33
+ "lines": 290,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 26100
37
+ },
38
+ {
39
+ "path": "doc/buildCondaDocs.sh",
40
+ "sha256": "414a253d48b776efa53213466e2026e564ab8cec809855dab5683104b6e503cf",
41
+ "language": "Shell",
42
+ "lines": 59,
43
+ "truncated": false,
44
+ "block": 4,
45
+ "row": 1892
46
+ },
47
+ {
48
+ "path": "doc/conf.py",
49
+ "sha256": "3aa6ad3411d1ce0901353a941b7f8cb0c073b3967e4324c7f4d9e182c5b105fc",
50
+ "language": "Python",
51
+ "lines": 190,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 24536
55
+ },
56
+ {
57
+ "path": "doc/demos/atacDemo.ipynb",
58
+ "sha256": "00c90ebe617938670017da66efb8574f6077a1726b508c65bd61ee3be48eebef",
59
+ "language": "Jupyter",
60
+ "lines": 988,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 7843
64
+ },
65
+ {
66
+ "path": "doc/demos/atac_process_bam.r",
67
+ "sha256": "d2e8242637b8e2d61ed504f6062ca930f7b23bb0b7749278ee4e9a92b2b91516",
68
+ "language": "R",
69
+ "lines": 248,
70
+ "truncated": false,
71
+ "block": 4,
72
+ "row": 982
73
+ },
74
+ {
75
+ "path": "doc/demos/documentationFigures.ipynb",
76
+ "sha256": "a3b01ff8f35138631af27cadf34ee2854a60bde08cdd08fab442c321b6104bbf",
77
+ "language": "Jupyter",
78
+ "lines": 526,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 7676
82
+ },
83
+ {
84
+ "path": "doc/demos/ga-demo.ipynb",
85
+ "sha256": "0e647880d1d04fadda0035170a32d580b95bb2dd3e325d7c50559f20cedc6136",
86
+ "language": "Jupyter",
87
+ "lines": 384,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 7765
91
+ },
92
+ {
93
+ "path": "doc/demos/mergeBigWig.py",
94
+ "sha256": "b5cd104b398f9c82e3eed2b2b89718c87ebb30689b9a9150d8b1ff8b55bd17ba",
95
+ "language": "Python",
96
+ "lines": 46,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 19807
100
+ },
101
+ {
102
+ "path": "doc/demos/osknAcceptance.ipynb",
103
+ "sha256": "07ff42592c173e797866f3f7012586758c9adcc5de1b7e9a6c0fa8103e91adc9",
104
+ "language": "Jupyter",
105
+ "lines": 1627,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 7859
109
+ },
110
+ {
111
+ "path": "doc/demos/osknExample.ipynb",
112
+ "sha256": "d67ff6335c3549efc91519e38e7812250bb0f7d93632889a80faa5ad19563a15",
113
+ "language": "Jupyter",
114
+ "lines": 1376,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 7851
118
+ },
119
+ {
120
+ "path": "doc/demos/runGa.py",
121
+ "sha256": "1766b09b5166096a5586fa0d00ec1069294200b447ed699e59ce83989fa2a701",
122
+ "language": "Python",
123
+ "lines": 101,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 21709
127
+ },
128
+ {
129
+ "path": "doc/demos/testIsm.py",
130
+ "sha256": "a166464360c119202c78edaccfe3b4e23f912553863ef865f9ccc91fa909a70c",
131
+ "language": "Python",
132
+ "lines": 88,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 22070
136
+ },
137
+ {
138
+ "path": "src/__init__.py",
139
+ "sha256": "7c4cf2cd950c7f443b64f577b57aafc927af801bb0fe8188e9fc33e17227e0b1",
140
+ "language": "Python",
141
+ "lines": 32,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 20466
145
+ },
146
+ {
147
+ "path": "src/bedUtils.py",
148
+ "sha256": "bbcb3997bf5bbd4ac890e34eeefff78896aa4e5c128f3c2bd617e0fb1870953f",
149
+ "language": "Python",
150
+ "lines": 498,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 27107
154
+ },
155
+ {
156
+ "path": "src/callbacks.py",
157
+ "sha256": "5a987a037b3d9c97d329177185fdfed71cea60dc845d423c2a2c69460a6c787f",
158
+ "language": "Python",
159
+ "lines": 809,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 27814
163
+ },
164
+ {
165
+ "path": "src/checkJson.py",
166
+ "sha256": "e24e60ecb8193efb816d0a0ffea096bb13604c0a36b0ec2f4a9c26f192b36ef5",
167
+ "language": "Python",
168
+ "lines": 68,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 21196
172
+ },
173
+ {
174
+ "path": "src/colors.py",
175
+ "sha256": "a11fbdc006df3ce28aae99317df03dc9674e83d2494231412039d1df6d9b076d",
176
+ "language": "Python",
177
+ "lines": 300,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 25638
181
+ },
182
+ {
183
+ "path": "src/gaOptimize.py",
184
+ "sha256": "893e127f94077bd5d09e940ee20d9f28a877cfbc81de9c0bd1090f16dd3244bb",
185
+ "language": "Python",
186
+ "lines": 1077,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 27955
190
+ },
191
+ {
192
+ "path": "src/generators.py",
193
+ "sha256": "b59d4c6564edb6786fa189f6f71d3adb495aab2791258a2b6780548b205df46f",
194
+ "language": "Python",
195
+ "lines": 147,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 24264
199
+ },
200
+ {
201
+ "path": "src/internal/constants.py",
202
+ "sha256": "a5c51c916dd89e6cb59d5ee53a028ef29e5315f856624876b7c6b420bf1289be",
203
+ "language": "Python",
204
+ "lines": 237,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 24581
208
+ },
209
+ {
210
+ "path": "src/internal/crashQueue.py",
211
+ "sha256": "66ae914bd1ea9008fdda9262f2fdce6cb09dc7e9dc3374d15762ded4b963e664",
212
+ "language": "Python",
213
+ "lines": 84,
214
+ "truncated": false,
215
+ "block": 3,
216
+ "row": 21249
217
+ },
218
+ {
219
+ "path": "src/internal/disableTensorflowLogging.py",
220
+ "sha256": "eea8a3d016d85be9d537f8b0908c8303058771dbb28fb593bbbc559fb9e899d5",
221
+ "language": "Python",
222
+ "lines": 96,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 21969
226
+ },
227
+ {
228
+ "path": "src/internal/files.py",
229
+ "sha256": "39306cac52231b77299fc985bd8b358ac66f791b43fc92ccc514363b05290155",
230
+ "language": "Python",
231
+ "lines": 27,
232
+ "truncated": false,
233
+ "block": 3,
234
+ "row": 19700
235
+ },
236
+ {
237
+ "path": "src/internal/interpretUtils.py",
238
+ "sha256": "0d9f329b83b024189342779af3f524700f5fd87cbdd3f97331ef3d28cfa1a490",
239
+ "language": "Python",
240
+ "lines": 1360,
241
+ "truncated": false,
242
+ "block": 3,
243
+ "row": 28038
244
+ },
245
+ {
246
+ "path": "src/internal/interpreter.py",
247
+ "sha256": "f049e7e38f0da3580ccc6e98cea97a9107f1da165b68a450da932ddd9fb5bb36",
248
+ "language": "Python",
249
+ "lines": 530,
250
+ "truncated": false,
251
+ "block": 3,
252
+ "row": 27120
253
+ },
254
+ {
255
+ "path": "src/internal/libjaccard.c",
256
+ "sha256": "5a7f0016b7d8a99688882c597c90409f8562f4ba43d64318ad7d0e3a415145eb",
257
+ "language": "C",
258
+ "lines": 120,
259
+ "truncated": false,
260
+ "block": 3,
261
+ "row": 148
262
+ },
263
+ {
264
+ "path": "src/internal/libslide.c",
265
+ "sha256": "37b694766f4d30b9b5bb0608ac197afd75b2c568d6638b67afdf5c50feec93a8",
266
+ "language": "C",
267
+ "lines": 92,
268
+ "truncated": false,
269
+ "block": 3,
270
+ "row": 120
271
+ },
272
+ {
273
+ "path": "src/internal/libushuffle.c",
274
+ "sha256": "41f314d38a15ef3be8bf58ec265485cef81e5d6471c12d065ad031d330f3c368",
275
+ "language": "C",
276
+ "lines": 344,
277
+ "truncated": false,
278
+ "block": 3,
279
+ "row": 229
280
+ },
281
+ {
282
+ "path": "src/internal/plotUtils.py",
283
+ "sha256": "991807744484b4dea6be426bf01dba131b27fa6944189b035926f0d10d9a767d",
284
+ "language": "Python",
285
+ "lines": 1288,
286
+ "truncated": false,
287
+ "block": 3,
288
+ "row": 28015
289
+ },
290
+ {
291
+ "path": "src/internal/predictUtils.py",
292
+ "sha256": "eccdbb112ec7a31ee4d8c9e111adc1c169520cf1a904afbcaacdc3c89bf6f2fa",
293
+ "language": "Python",
294
+ "lines": 308,
295
+ "truncated": false,
296
+ "block": 3,
297
+ "row": 26426
298
+ },
299
+ {
300
+ "path": "src/internal/shap.py",
301
+ "sha256": "b1ae6cfa726be11281fac550633d8ba4747b1e210ba04a130d04df528892ba58",
302
+ "language": "Python",
303
+ "lines": 815,
304
+ "truncated": false,
305
+ "block": 3,
306
+ "row": 27739
307
+ },
308
+ {
309
+ "path": "src/interpretFlat.py",
310
+ "sha256": "c909ab036d4fb6e8215d239501682fd77bd6c13eba76026f2e1ffd25bb3cb678",
311
+ "language": "Python",
312
+ "lines": 352,
313
+ "truncated": false,
314
+ "block": 3,
315
+ "row": 26575
316
+ },
317
+ {
318
+ "path": "src/interpretPisa.py",
319
+ "sha256": "1c7c3933e25917371c982d9746351e31e256b5bd0d090ad4dae5419acdfbf66a",
320
+ "language": "Python",
321
+ "lines": 269,
322
+ "truncated": false,
323
+ "block": 3,
324
+ "row": 25943
325
+ },
326
+ {
327
+ "path": "src/jaccard.py",
328
+ "sha256": "63cdb5780f55d036f2b1e36cfd5cb5ebaa5eec8159ba4d4eb3f4838436b200d6",
329
+ "language": "Python",
330
+ "lines": 73,
331
+ "truncated": false,
332
+ "block": 3,
333
+ "row": 21494
334
+ },
335
+ {
336
+ "path": "src/layers.py",
337
+ "sha256": "d5bf25423ecce5bd5e1d988b74a20c262f6c5735861f930dd4578e6c6fa113cf",
338
+ "language": "Python",
339
+ "lines": 139,
340
+ "truncated": false,
341
+ "block": 3,
342
+ "row": 23496
343
+ },
344
+ {
345
+ "path": "src/lengthCalc.py",
346
+ "sha256": "faeffd0f5496de378fb036a4774c1c8d6851f98024d0eda75840b05ef9de0ed4",
347
+ "language": "Python",
348
+ "lines": 206,
349
+ "truncated": false,
350
+ "block": 3,
351
+ "row": 25271
352
+ },
353
+ {
354
+ "path": "src/logUtils.py",
355
+ "sha256": "198353b1ef5a3da1ccf3bce216b484a643a3017e5cff432833ed418d76ee308d",
356
+ "language": "Python",
357
+ "lines": 373,
358
+ "truncated": false,
359
+ "block": 3,
360
+ "row": 26255
361
+ },
362
+ {
363
+ "path": "src/losses.py",
364
+ "sha256": "76dc28be79051d6d3aaa6d361c20633e3b2c7933ddb2434a5c891a765b523ace",
365
+ "language": "Python",
366
+ "lines": 91,
367
+ "truncated": false,
368
+ "block": 3,
369
+ "row": 22405
370
+ },
371
+ {
372
+ "path": "src/makeLossPlots.py",
373
+ "sha256": "d37e2ade0ff3c28362dca2ae3a0c560efdece637e1ade3dbede583f4f13cb191",
374
+ "language": "Python",
375
+ "lines": 184,
376
+ "truncated": false,
377
+ "block": 3,
378
+ "row": 24606
379
+ },
380
+ {
381
+ "path": "src/makePisaFigure.py",
382
+ "sha256": "fcd7e3d67edb1e9ec3f9d90d66b8f788300892ea3f035a90f8c0f22e86729fa0",
383
+ "language": "Python",
384
+ "lines": 105,
385
+ "truncated": false,
386
+ "block": 3,
387
+ "row": 22075
388
+ },
389
+ {
390
+ "path": "src/makePredictions.py",
391
+ "sha256": "de9f5165cba41ea66a06b533d06706f2e9a676aca2212fd38d96d76189e5aecb",
392
+ "language": "Python",
393
+ "lines": 266,
394
+ "truncated": false,
395
+ "block": 3,
396
+ "row": 25707
397
+ },
398
+ {
399
+ "path": "src/makePredictionsBed.py",
400
+ "sha256": "de9f5165cba41ea66a06b533d06706f2e9a676aca2212fd38d96d76189e5aecb",
401
+ "language": "Python",
402
+ "lines": 266,
403
+ "truncated": false,
404
+ "block": 3,
405
+ "row": 25707
406
+ },
407
+ {
408
+ "path": "src/makePredictionsFasta.py",
409
+ "sha256": "de9f5165cba41ea66a06b533d06706f2e9a676aca2212fd38d96d76189e5aecb",
410
+ "language": "Python",
411
+ "lines": 266,
412
+ "truncated": false,
413
+ "block": 3,
414
+ "row": 25707
415
+ },
416
+ {
417
+ "path": "src/metrics.py",
418
+ "sha256": "829f8d999e7cd342fe8317bc0f9cc1558f83a69292a6d9b14a2b9e0755bc1836",
419
+ "language": "Python",
420
+ "lines": 483,
421
+ "truncated": false,
422
+ "block": 3,
423
+ "row": 27060
424
+ },
425
+ {
426
+ "path": "src/models.py",
427
+ "sha256": "152389313dde2c05ed5013f8634903931ca564cdb8b4d7100cb1d31e609e859c",
428
+ "language": "Python",
429
+ "lines": 417,
430
+ "truncated": false,
431
+ "block": 3,
432
+ "row": 27180
433
+ },
434
+ {
435
+ "path": "src/motifAddQuantiles.py",
436
+ "sha256": "efce8e108bd764c59f8ae78a7256fd79a9e2ebb7dcff900d92c1da560dd4e311",
437
+ "language": "Python",
438
+ "lines": 371,
439
+ "truncated": false,
440
+ "block": 3,
441
+ "row": 26619
442
+ },
443
+ {
444
+ "path": "src/motifScan.py",
445
+ "sha256": "adf286b5c6f9a907454d146508a1c22a5e33043a7dbc8c84c387ce54653a353d",
446
+ "language": "Python",
447
+ "lines": 194,
448
+ "truncated": false,
449
+ "block": 3,
450
+ "row": 24459
451
+ },
452
+ {
453
+ "path": "src/motifSeqletCutoffs.py",
454
+ "sha256": "f8f2be96ac2853f9500ddbaa6b0b38f6bcbcb412f8be9366e53ea039515783c8",
455
+ "language": "Python",
456
+ "lines": 182,
457
+ "truncated": false,
458
+ "block": 3,
459
+ "row": 24558
460
+ },
461
+ {
462
+ "path": "src/motifUtils.py",
463
+ "sha256": "1303ea2e179eff4679d63556f81d85233646aeff499db9d1266686adac8abaed",
464
+ "language": "Python",
465
+ "lines": 1443,
466
+ "truncated": false,
467
+ "block": 4,
468
+ "row": 18
469
+ },
470
+ {
471
+ "path": "src/plotting.py",
472
+ "sha256": "1d90b7af64ffc375ccc1c57f2cb4812a7345f8ee02e7efc50ae10f8bcdd49ea8",
473
+ "language": "Python",
474
+ "lines": 994,
475
+ "truncated": false,
476
+ "block": 3,
477
+ "row": 27901
478
+ },
479
+ {
480
+ "path": "src/predictToBigwig.py",
481
+ "sha256": "1a0a8dae87a330263d1a9566aa78dd9741555c03ed84074be98cd1b64294ff7e",
482
+ "language": "Python",
483
+ "lines": 296,
484
+ "truncated": false,
485
+ "block": 3,
486
+ "row": 26112
487
+ },
488
+ {
489
+ "path": "src/prepareBed.py",
490
+ "sha256": "e1da92955e19678f132dc4039b9f70b0e688980e687d4c38d7fdd027bf15e0ce",
491
+ "language": "Python",
492
+ "lines": 704,
493
+ "truncated": false,
494
+ "block": 3,
495
+ "row": 27688
496
+ },
497
+ {
498
+ "path": "src/prepareTrainingData.py",
499
+ "sha256": "3c0aea0fcae6a9697a3d15acf74de085dd4a60a54383933d4b160a93ac9b0670",
500
+ "language": "Python",
501
+ "lines": 254,
502
+ "truncated": false,
503
+ "block": 3,
504
+ "row": 25654
505
+ },
506
+ {
507
+ "path": "src/schema.py",
508
+ "sha256": "761a39a0d53df2e1cef3b533efedb0c850e2e36b8bd491f56c8a98c89f48a51d",
509
+ "language": "Python",
510
+ "lines": 156,
511
+ "truncated": false,
512
+ "block": 3,
513
+ "row": 27793
514
+ },
515
+ {
516
+ "path": "src/schematools/build.py",
517
+ "sha256": "e44ff992ac1e84a4f3189b84285acb28997fcdc2d3358c17a8bde7ed4e3f6f51",
518
+ "language": "Python",
519
+ "lines": 110,
520
+ "truncated": false,
521
+ "block": 3,
522
+ "row": 22646
523
+ },
524
+ {
525
+ "path": "src/schematools/runTest.py",
526
+ "sha256": "1bbd38dc29664ddc5262d8e7e933fca2d3a3fc3c4e65f0ec54ba087ee454d4f3",
527
+ "language": "Python",
528
+ "lines": 58,
529
+ "truncated": false,
530
+ "block": 3,
531
+ "row": 20997
532
+ },
533
+ {
534
+ "path": "src/shapToBigwig.py",
535
+ "sha256": "c6a5c66408a9a06dbc4e81bc549745648453f96a07ca3070f12002ba91cd36c7",
536
+ "language": "Python",
537
+ "lines": 175,
538
+ "truncated": false,
539
+ "block": 3,
540
+ "row": 24402
541
+ },
542
+ {
543
+ "path": "src/shapToNumpy.py",
544
+ "sha256": "6be10837a915a8ce28362af68d01a25994856ca8b6b2e5d1f24923b0771a38b3",
545
+ "language": "Python",
546
+ "lines": 72,
547
+ "truncated": false,
548
+ "block": 3,
549
+ "row": 21515
550
+ },
551
+ {
552
+ "path": "src/showModel.py",
553
+ "sha256": "ce0fdd9d5746996d5996837acffa36c4bfc680e1e5d150dfb8e41b026a4c4889",
554
+ "language": "Python",
555
+ "lines": 69,
556
+ "truncated": false,
557
+ "block": 3,
558
+ "row": 21696
559
+ },
560
+ {
561
+ "path": "src/showTrainingProgress.py",
562
+ "sha256": "c6dfa524a9a1ab0916d4aeae45b25e7976d1699069db64a2566a7b0d696d6d40",
563
+ "language": "Python",
564
+ "lines": 471,
565
+ "truncated": false,
566
+ "block": 3,
567
+ "row": 27129
568
+ },
569
+ {
570
+ "path": "src/tools/addNoise.py",
571
+ "sha256": "f3ae19d0d17bbedfd73ad342ad3400674243f623e816c947f54cbe9d29b81051",
572
+ "language": "Python",
573
+ "lines": 118,
574
+ "truncated": false,
575
+ "block": 3,
576
+ "row": 22857
577
+ },
578
+ {
579
+ "path": "src/tools/addNoiseUtils.py",
580
+ "sha256": "4c5355d09d11ad07717b40dafce49c4cd961def620296e9d47cad259cf1e8076",
581
+ "language": "Python",
582
+ "lines": 232,
583
+ "truncated": false,
584
+ "block": 3,
585
+ "row": 25628
586
+ },
587
+ {
588
+ "path": "src/tools/bestMotifsOnly.py",
589
+ "sha256": "8dd87bf19f408f029a00e3754c43385e63ed42308f0b7014696a2bf75f19252c",
590
+ "language": "Python",
591
+ "lines": 271,
592
+ "truncated": false,
593
+ "block": 3,
594
+ "row": 26026
595
+ },
596
+ {
597
+ "path": "src/tools/filterProc.py",
598
+ "sha256": "f9520c1c427c41c1e6eaf797c866022f2efa0beb497d12bb7d102149f7f66fbb",
599
+ "language": "Python",
600
+ "lines": 141,
601
+ "truncated": false,
602
+ "block": 3,
603
+ "row": 22832
604
+ },
605
+ {
606
+ "path": "src/tools/gcContents.py",
607
+ "sha256": "67b55171e39334f7f4f8670ec4b6009e45c55879022aafb08f19721eae06e1a6",
608
+ "language": "Python",
609
+ "lines": 222,
610
+ "truncated": false,
611
+ "block": 3,
612
+ "row": 24746
613
+ },
614
+ {
615
+ "path": "src/tools/lossWeights.py",
616
+ "sha256": "2f17ad25c0a338daec600de82a838b100cd0d1717135ab7b88babca60be46beb",
617
+ "language": "Python",
618
+ "lines": 120,
619
+ "truncated": false,
620
+ "block": 3,
621
+ "row": 23474
622
+ },
623
+ {
624
+ "path": "src/tools/plots.py",
625
+ "sha256": "bf6ae6824b7d78e5f0f53fc8b86f4c14ac88640ada901473b9581d246bd0f060",
626
+ "language": "Python",
627
+ "lines": 1061,
628
+ "truncated": false,
629
+ "block": 3,
630
+ "row": 27951
631
+ },
632
+ {
633
+ "path": "src/tools/revcompTools.py",
634
+ "sha256": "947a8e4bf9dd7ad74ec172d5fa9768fcd090c2b6e89c9f0ac394a57df1bafabf",
635
+ "language": "Python",
636
+ "lines": 92,
637
+ "truncated": false,
638
+ "block": 3,
639
+ "row": 22655
640
+ },
641
+ {
642
+ "path": "src/tools/shiftBigwigs.py",
643
+ "sha256": "a5c6eca85d1594e4cf04cfb59056774543dbf616820f552055585264c1a97d3c",
644
+ "language": "Python",
645
+ "lines": 99,
646
+ "truncated": false,
647
+ "block": 3,
648
+ "row": 22174
649
+ },
650
+ {
651
+ "path": "src/tools/shiftPisa.py",
652
+ "sha256": "ad3eab3a842941bd5f376899f560a83d91a4c88f518a83578771f577fc9963c0",
653
+ "language": "Python",
654
+ "lines": 173,
655
+ "truncated": false,
656
+ "block": 3,
657
+ "row": 24449
658
+ },
659
+ {
660
+ "path": "src/tools/slurm.py",
661
+ "sha256": "8a129b25e9c6dc5a6748e4f50212f8565cfcbfb1546f48a22480fabb58ab7035",
662
+ "language": "Python",
663
+ "lines": 348,
664
+ "truncated": false,
665
+ "block": 3,
666
+ "row": 26504
667
+ },
668
+ {
669
+ "path": "src/tools/tileGenome.py",
670
+ "sha256": "c3ef9003d7844977770148d797f4523c13cb34d68c4284400aa295dd38ffce90",
671
+ "language": "Python",
672
+ "lines": 82,
673
+ "truncated": false,
674
+ "block": 3,
675
+ "row": 22256
676
+ },
677
+ {
678
+ "path": "src/trainCombinedModel.py",
679
+ "sha256": "767e744e4f5d05ed301c4a8797600a001a9364a0db20cc5b1161b5d12c38f008",
680
+ "language": "Python",
681
+ "lines": 116,
682
+ "truncated": false,
683
+ "block": 3,
684
+ "row": 22887
685
+ },
686
+ {
687
+ "path": "src/trainSoloModel.py",
688
+ "sha256": "0d46eab5738f2055a12546f8455f4b55ae540630f08494cf612521ce6d7d95ef",
689
+ "language": "Python",
690
+ "lines": 205,
691
+ "truncated": false,
692
+ "block": 3,
693
+ "row": 24975
694
+ },
695
+ {
696
+ "path": "src/trainTransformationModel.py",
697
+ "sha256": "1073f52b6902865697643588d48df1d898e3481ce17dd01607a2b06074fc6ad8",
698
+ "language": "Python",
699
+ "lines": 122,
700
+ "truncated": false,
701
+ "block": 3,
702
+ "row": 22825
703
+ },
704
+ {
705
+ "path": "src/training.py",
706
+ "sha256": "0417588c0b5ef4d4ca31a28fa5d2bd3a2595ce978d335606b795d2b220e6af06",
707
+ "language": "Python",
708
+ "lines": 176,
709
+ "truncated": false,
710
+ "block": 3,
711
+ "row": 24794
712
+ },
713
+ {
714
+ "path": "src/ushuffle.py",
715
+ "sha256": "be3d04810e7af4b30d43410f26d255b1f649a626658bf06e2cc8f7e953dff86b",
716
+ "language": "Python",
717
+ "lines": 82,
718
+ "truncated": false,
719
+ "block": 3,
720
+ "row": 22281
721
+ },
722
+ {
723
+ "path": "src/utils.py",
724
+ "sha256": "867fcaddcd38e95aeb4d7b9700f66012db8e1101755b6ac10b39a67c4c2cb0bb",
725
+ "language": "Python",
726
+ "lines": 1572,
727
+ "truncated": false,
728
+ "block": 4,
729
+ "row": 31
730
+ }
731
+ ]
732
+ }
manifests/fc/github.com__zhou-1314__garfield-reproducibility.json ADDED
@@ -0,0 +1,552 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/zhou-1314/garfield-reproducibility",
4
+ "url": "https://github.com/zhou-1314/Garfield-reproducibility",
5
+ "host": "github.com",
6
+ "commit": "1b7435897ca744bfea09d7ad04590b8cdfd2c0c8",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "Garfield-garfield_dev/Garfield/__init__.py",
13
+ "sha256": "dbfc74c70c7af0456454988c8050b637b519f7837695571f608e60f736d45670",
14
+ "language": "Python",
15
+ "lines": 9,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 18420
19
+ },
20
+ {
21
+ "path": "Garfield-garfield_dev/Garfield/_settings.py",
22
+ "sha256": "4935658b18cb45aad8d94a696bfa94177728da466bd7e17c76447d72f5eeaf52",
23
+ "language": "Python",
24
+ "lines": 319,
25
+ "truncated": false,
26
+ "block": 3,
27
+ "row": 25938
28
+ },
29
+ {
30
+ "path": "Garfield-garfield_dev/Garfield/_version.py",
31
+ "sha256": "6d4ea1f9d2df10fcab7ad97ca6ba128d2968e4d5fd8d0f348fd98bcd460ad6f6",
32
+ "language": "Python",
33
+ "lines": 2,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 17417
37
+ },
38
+ {
39
+ "path": "Garfield-garfield_dev/Garfield/analysis/__init__.py",
40
+ "sha256": "d203d60e184a9b37eaa0aaba65101857738c712478a5625f67c483beede54523",
41
+ "language": "Python",
42
+ "lines": 7,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 17936
46
+ },
47
+ {
48
+ "path": "Garfield-garfield_dev/Garfield/analysis/calc_neighbor_prop.py",
49
+ "sha256": "ba32e856d48f04d29f3bbaf4ab10e07094b364e6e85477c18d3fb68ee0466b14",
50
+ "language": "Python",
51
+ "lines": 75,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 21118
55
+ },
56
+ {
57
+ "path": "Garfield-garfield_dev/Garfield/analysis/calc_niches_enrich.py",
58
+ "sha256": "7217aac5e83cfc7e68e5ae1ae77c933d11f82c1bd0e67242810f5008a12b4b39",
59
+ "language": "Python",
60
+ "lines": 215,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 24633
64
+ },
65
+ {
66
+ "path": "Garfield-garfield_dev/Garfield/analysis/calc_niches_marker.py",
67
+ "sha256": "c286cc3ac65867628e8bb013e490e3f8fb266b903a34d5a84037a57ef4246dea",
68
+ "language": "Python",
69
+ "lines": 269,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 25685
73
+ },
74
+ {
75
+ "path": "Garfield-garfield_dev/Garfield/model/Garfield.py",
76
+ "sha256": "18394b9fa8a4a00a55929f9573a027406cb2d9ea44da6e6524b2bedb6e8dbee8",
77
+ "language": "Python",
78
+ "lines": 1065,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 27895
82
+ },
83
+ {
84
+ "path": "Garfield-garfield_dev/Garfield/model/__init__.py",
85
+ "sha256": "d33a4335a3f387074fea292bfeb61df2a89549c15ac8e2ce8bee94123171c704",
86
+ "language": "Python",
87
+ "lines": 4,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 17583
91
+ },
92
+ {
93
+ "path": "Garfield-garfield_dev/Garfield/model/basemodelmixin.py",
94
+ "sha256": "9b4062f1bfc1cf18b4c5ea69ccddb67f07ef38bfc1f4f4119481db75dcaab953",
95
+ "language": "Python",
96
+ "lines": 360,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 26136
100
+ },
101
+ {
102
+ "path": "Garfield-garfield_dev/Garfield/model/utils.py",
103
+ "sha256": "0249cdb8af0f17db903ad49f8edc2d37a6795e9b69f282135ee735757d9c2c6b",
104
+ "language": "Python",
105
+ "lines": 348,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 25982
109
+ },
110
+ {
111
+ "path": "Garfield-garfield_dev/Garfield/modules/GNNModelVAE.py",
112
+ "sha256": "6ebfc46d179c9d8dd9adf4331482d00a35fdb0e80de7f45977b36390a274cf8c",
113
+ "language": "Python",
114
+ "lines": 530,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 27292
118
+ },
119
+ {
120
+ "path": "Garfield-garfield_dev/Garfield/modules/__init__.py",
121
+ "sha256": "e02be55303deead177e18a83602f92f3a6d00e1ceb593c87b5d1648d3635b27f",
122
+ "language": "Python",
123
+ "lines": 18,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 18318
127
+ },
128
+ {
129
+ "path": "Garfield-garfield_dev/Garfield/modules/loss.py",
130
+ "sha256": "5550b79b280162280c2dfda330e2a14859b49396b167faa9834d17e0c7c3e872",
131
+ "language": "Python",
132
+ "lines": 335,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 25405
136
+ },
137
+ {
138
+ "path": "Garfield-garfield_dev/Garfield/modules/utils.py",
139
+ "sha256": "ea6c125f3cbb98c83e8a24446157981267be75972b83d5b45e1e2dd9bc2eff54",
140
+ "language": "Python",
141
+ "lines": 55,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 20204
145
+ },
146
+ {
147
+ "path": "Garfield-garfield_dev/Garfield/nn/__init__.py",
148
+ "sha256": "b7e3e7edec3fe4cf6cde8897d6b541a42b3415dc3983c580d04409dabff82fd2",
149
+ "language": "Python",
150
+ "lines": 5,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 17701
154
+ },
155
+ {
156
+ "path": "Garfield-garfield_dev/Garfield/nn/decoders.py",
157
+ "sha256": "bfd6f17c8833ec0c4e21cf22d2d2cb46ade0c1f96194bf4aac089bc918b2753f",
158
+ "language": "Python",
159
+ "lines": 334,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 25824
163
+ },
164
+ {
165
+ "path": "Garfield-garfield_dev/Garfield/nn/encoders.py",
166
+ "sha256": "f26fa7338d1aa4e03257746ad2bce6bbbf694f897efcf965caef6ea472b342b5",
167
+ "language": "Python",
168
+ "lines": 407,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 26474
172
+ },
173
+ {
174
+ "path": "Garfield-garfield_dev/Garfield/nn/utils.py",
175
+ "sha256": "5c9abbe06c5d6746844072eb47f218d4bca0165db466f285ab1fe48899fa23bd",
176
+ "language": "Python",
177
+ "lines": 104,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 21436
181
+ },
182
+ {
183
+ "path": "Garfield-garfield_dev/Garfield/plot/__init__.py",
184
+ "sha256": "9b790f9f94ad11bf3d02d41a68d2706bfd9052bf2d949a09286accbe773b8241",
185
+ "language": "Python",
186
+ "lines": 8,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 17644
190
+ },
191
+ {
192
+ "path": "Garfield-garfield_dev/Garfield/plot/spatial_plot.py",
193
+ "sha256": "096fe826b7cbec1fdb97090416b87943d99df09868a2d11c6a1baf391c6b8de8",
194
+ "language": "Python",
195
+ "lines": 812,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 27476
199
+ },
200
+ {
201
+ "path": "Garfield-garfield_dev/Garfield/preprocessing/__init__.py",
202
+ "sha256": "8ce40d6689eacbc401ad5f4fce8f53f5035ad49dfd09a9dfcf090318a299abbd",
203
+ "language": "Python",
204
+ "lines": 8,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 17658
208
+ },
209
+ {
210
+ "path": "Garfield-garfield_dev/Garfield/preprocessing/_graph.py",
211
+ "sha256": "d2b74634bb2f6e10716e1516e94ec7e6633f75fb0e39e9eff4909efd3809c383",
212
+ "language": "Python",
213
+ "lines": 61,
214
+ "truncated": false,
215
+ "block": 3,
216
+ "row": 20330
217
+ },
218
+ {
219
+ "path": "Garfield-garfield_dev/Garfield/preprocessing/_utils.py",
220
+ "sha256": "7001586fea9a2e2b1758dea3a6faccef860de9c21d2225b22ee554debbf0fc6e",
221
+ "language": "Python",
222
+ "lines": 961,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 27651
226
+ },
227
+ {
228
+ "path": "Garfield-garfield_dev/Garfield/preprocessing/adj_construction.py",
229
+ "sha256": "1ba120de1e330aa7a5e3c71d2daeaf6e811a62314b0c1f29f6f4bea789a09281",
230
+ "language": "Python",
231
+ "lines": 1077,
232
+ "truncated": false,
233
+ "block": 3,
234
+ "row": 27842
235
+ },
236
+ {
237
+ "path": "Garfield-garfield_dev/Garfield/preprocessing/adj_construction_optimized.py",
238
+ "sha256": "d209fcbcbc95beb1b3a2cf5640ed523a61e021a7e9d662d5a4d41e416144ab47",
239
+ "language": "Python",
240
+ "lines": 385,
241
+ "truncated": false,
242
+ "block": 3,
243
+ "row": 26049
244
+ },
245
+ {
246
+ "path": "Garfield-garfield_dev/Garfield/preprocessing/match_utils.py",
247
+ "sha256": "15379accfe4618707c76ea5752ed00dc15e2da4f5b5253a77dc1edf03dc9170e",
248
+ "language": "Python",
249
+ "lines": 450,
250
+ "truncated": false,
251
+ "block": 3,
252
+ "row": 26563
253
+ },
254
+ {
255
+ "path": "Garfield-garfield_dev/Garfield/preprocessing/preprocess.py",
256
+ "sha256": "df762147b7c682f6ecf149d7f6949173e668b0463c8d2f7caed8e66838c3a5d6",
257
+ "language": "Python",
258
+ "lines": 223,
259
+ "truncated": false,
260
+ "block": 3,
261
+ "row": 24820
262
+ },
263
+ {
264
+ "path": "Garfield-garfield_dev/Garfield/preprocessing/preprocess_utils.py",
265
+ "sha256": "c9c88819c7485e5619974f532a89e29a06d6f32092e408b6d6ed9b4d62f3b8ac",
266
+ "language": "Python",
267
+ "lines": 1252,
268
+ "truncated": false,
269
+ "block": 3,
270
+ "row": 27984
271
+ },
272
+ {
273
+ "path": "Garfield-garfield_dev/Garfield/trainer/__init__.py",
274
+ "sha256": "86cb4f43938ebadfcb28b63e34b5bb9133af8278c76ab358f20d90fb3d65767a",
275
+ "language": "Python",
276
+ "lines": 13,
277
+ "truncated": false,
278
+ "block": 3,
279
+ "row": 17971
280
+ },
281
+ {
282
+ "path": "Garfield-garfield_dev/Garfield/trainer/basetrainermixin.py",
283
+ "sha256": "d074076a7ff37f6a96160714b92dc10bf7d81f3c94c1304b703ba0e4ec99c0fd",
284
+ "language": "Python",
285
+ "lines": 148,
286
+ "truncated": false,
287
+ "block": 3,
288
+ "row": 23186
289
+ },
290
+ {
291
+ "path": "Garfield-garfield_dev/Garfield/trainer/custom_callbacks.py",
292
+ "sha256": "f913791f5551b27c07261a211c8b354e066340f86813ec8d6b43f831875bf714",
293
+ "language": "Python",
294
+ "lines": 174,
295
+ "truncated": false,
296
+ "block": 3,
297
+ "row": 23170
298
+ },
299
+ {
300
+ "path": "Garfield-garfield_dev/Garfield/trainer/lightning_module.py",
301
+ "sha256": "22aa76225052d6c5f0ba91ee857300f797d27f7940d28cae4706e4e6af04e2a9",
302
+ "language": "Python",
303
+ "lines": 268,
304
+ "truncated": false,
305
+ "block": 3,
306
+ "row": 25247
307
+ },
308
+ {
309
+ "path": "Garfield-garfield_dev/Garfield/trainer/metrics.py",
310
+ "sha256": "44f38e7b95ebe277d9ecd2436867f6214bb6b91de721e5337f7a2751b538badf",
311
+ "language": "Python",
312
+ "lines": 119,
313
+ "truncated": false,
314
+ "block": 3,
315
+ "row": 22392
316
+ },
317
+ {
318
+ "path": "Garfield-garfield_dev/Garfield/trainer/trainer.py",
319
+ "sha256": "87ebc177e76a649f4beb7b2681e4e3d2a0158a77966b6ce23957b94a24473559",
320
+ "language": "Python",
321
+ "lines": 727,
322
+ "truncated": false,
323
+ "block": 3,
324
+ "row": 27567
325
+ },
326
+ {
327
+ "path": "Garfield-garfield_dev/Garfield/trainer/utils.py",
328
+ "sha256": "47d67b374dc3930c02105e9ae8a4570925aec717c4ef307a71b1d2393ac0863a",
329
+ "language": "Python",
330
+ "lines": 223,
331
+ "truncated": false,
332
+ "block": 3,
333
+ "row": 24164
334
+ },
335
+ {
336
+ "path": "LICENSE",
337
+ "sha256": "91309146ccfeecf1290abed6faec409a7cab5968d21bbfbaaf7264be75bd4545",
338
+ "language": "License",
339
+ "lines": 21,
340
+ "truncated": false,
341
+ "block": 3,
342
+ "row": 7979
343
+ },
344
+ {
345
+ "path": "README.md",
346
+ "sha256": "b37aa72c4d034698308cf434e7ad7f523ef3adeb32665d91c815b1f01f8c911e",
347
+ "language": "Text",
348
+ "lines": 149,
349
+ "truncated": false,
350
+ "block": 4,
351
+ "row": 2606
352
+ },
353
+ {
354
+ "path": "benchmark_tissue_niches_analysis.ipynb",
355
+ "sha256": "b2cdda342e7023584dc78c07aa2df46e5e2547d9e6403fda86199bfc95891464",
356
+ "language": "Jupyter",
357
+ "lines": 1276,
358
+ "truncated": false,
359
+ "block": 3,
360
+ "row": 7842
361
+ },
362
+ {
363
+ "path": "benchmarking/ablation_study.py",
364
+ "sha256": "075240984d50ca3c3c7390c8a4b7c68ab9937a98a8a6aa5c635a597b379a289a",
365
+ "language": "Python",
366
+ "lines": 714,
367
+ "truncated": false,
368
+ "block": 3,
369
+ "row": 26954
370
+ },
371
+ {
372
+ "path": "benchmarking/ablation_weight_parameter.py",
373
+ "sha256": "069d47ab26a297f8d1c677148747441d19323bb68754a5e27eaf22e753cb997b",
374
+ "language": "Python",
375
+ "lines": 473,
376
+ "truncated": false,
377
+ "block": 3,
378
+ "row": 26209
379
+ },
380
+ {
381
+ "path": "benchmarking/benchmark_spatial_scalability.py",
382
+ "sha256": "25285ee198e71ef55f7bd9a3923341895d2bbd2850780eb518d184eaf01f89d8",
383
+ "language": "Python",
384
+ "lines": 523,
385
+ "truncated": false,
386
+ "block": 3,
387
+ "row": 26377
388
+ },
389
+ {
390
+ "path": "benchmarking/benchmark_utils.py",
391
+ "sha256": "02d6d4c6b543cd6880ab696455182f76ba114aabeb8ddee4366c85fd1c2724cf",
392
+ "language": "Python",
393
+ "lines": 367,
394
+ "truncated": false,
395
+ "block": 3,
396
+ "row": 25390
397
+ },
398
+ {
399
+ "path": "benchmarking/plot_ablation_results.py",
400
+ "sha256": "6b1bdfe61cff898a1e50f6a79477c4238ace4d12eb8621c7c93e2f64b56d7bea",
401
+ "language": "Python",
402
+ "lines": 461,
403
+ "truncated": false,
404
+ "block": 3,
405
+ "row": 26610
406
+ },
407
+ {
408
+ "path": "benchmarking/plot_benchmark_results.py",
409
+ "sha256": "e6fde1b408b38d0a92ac500436c6bdeef06e18257dda7dd72c2f69e4dbd69179",
410
+ "language": "Python",
411
+ "lines": 547,
412
+ "truncated": false,
413
+ "block": 3,
414
+ "row": 26913
415
+ },
416
+ {
417
+ "path": "benchmarking/plot_weight_ablation.py",
418
+ "sha256": "1873a85fc801a4318ddc12984d55b3605191ed9fbcd84ee6d057191fb11404c2",
419
+ "language": "Python",
420
+ "lines": 413,
421
+ "truncated": false,
422
+ "block": 3,
423
+ "row": 26559
424
+ },
425
+ {
426
+ "path": "benchmarking/run_ablation.sh",
427
+ "sha256": "adbd074271293fc7affb584f4ec3ae0718a4ad9f60c1d49f96f758107bbe40c2",
428
+ "language": "Shell",
429
+ "lines": 215,
430
+ "truncated": false,
431
+ "block": 4,
432
+ "row": 2210
433
+ },
434
+ {
435
+ "path": "benchmarking/run_benchmark.sh",
436
+ "sha256": "bfcc9b906bf3bf247916e7dd61c0febfe4ad0dee362f84aed28dded984f9eabe",
437
+ "language": "Shell",
438
+ "lines": 200,
439
+ "truncated": false,
440
+ "block": 4,
441
+ "row": 2215
442
+ },
443
+ {
444
+ "path": "benchmarking/run_weight_ablation.sh",
445
+ "sha256": "04c9bc0aa97dae5e0d70b74af4f3d83a2734401d45daecaf8929b101adff97a2",
446
+ "language": "Shell",
447
+ "lines": 247,
448
+ "truncated": false,
449
+ "block": 4,
450
+ "row": 2227
451
+ },
452
+ {
453
+ "path": "benchmarking/train_multi_gpu.py",
454
+ "sha256": "57d9912a842fafd9d3db9b6c07f131b625a12dbafca15978b6b59e68d69b1533",
455
+ "language": "Python",
456
+ "lines": 215,
457
+ "truncated": false,
458
+ "block": 3,
459
+ "row": 23951
460
+ },
461
+ {
462
+ "path": "benchmarking/train_multi_gpu_torchrun.py",
463
+ "sha256": "7f06438c54e49942fe4bcbc9ad3f6fbaf070af8a122f914471690260067bee6f",
464
+ "language": "Python",
465
+ "lines": 234,
466
+ "truncated": false,
467
+ "block": 3,
468
+ "row": 24068
469
+ },
470
+ {
471
+ "path": "data_preparation.ipynb",
472
+ "sha256": "cbac73be1757a2780739686b6efc90763f74718f4e5363f277c35c017a5bfb9d",
473
+ "language": "Jupyter",
474
+ "lines": 2323,
475
+ "truncated": false,
476
+ "block": 3,
477
+ "row": 7884
478
+ },
479
+ {
480
+ "path": "paper_analyses/additional_spatial_analyses/01.Garfield_spatial_molecular_niche_seqFISH.ipynb",
481
+ "sha256": "724d60b258e0f5229113d9bbf9cc96d026da13753df961cd5f5dd53a38846413",
482
+ "language": "Jupyter",
483
+ "lines": 366,
484
+ "truncated": false,
485
+ "block": 3,
486
+ "row": 7590
487
+ },
488
+ {
489
+ "path": "paper_analyses/additional_spatial_analyses/02.Garfield_spatia_molecular_niche_analysis.ipynb",
490
+ "sha256": "51c1251e722a4ce5856e544515d158fb5626fb8a5adb7200c1e9233e8781ab2c",
491
+ "language": "Jupyter",
492
+ "lines": 226,
493
+ "truncated": false,
494
+ "block": 3,
495
+ "row": 7405
496
+ },
497
+ {
498
+ "path": "paper_analyses/additional_spatial_analyses/02.Garfield_spatial_niche_analysis2.ipynb",
499
+ "sha256": "333af307b8924053298630ac6ae74f81277f4602aa76ce44c2bbeb3721ae518c",
500
+ "language": "Jupyter",
501
+ "lines": 387,
502
+ "truncated": false,
503
+ "block": 3,
504
+ "row": 7612
505
+ },
506
+ {
507
+ "path": "paper_analyses/additional_spatial_analyses/03.metrics_benchmark.ipynb",
508
+ "sha256": "daf0cb104f5d3023cc1e8e3a68419c1483fb46be451edf02720bf5f5515eabd5",
509
+ "language": "Jupyter",
510
+ "lines": 227,
511
+ "truncated": false,
512
+ "block": 3,
513
+ "row": 7565
514
+ },
515
+ {
516
+ "path": "paper_analyses/data_preparation/00.data_prep.ipynb",
517
+ "sha256": "f5d63370f77463abfa3131964d41f84580a678d4683cda4c0416fb4e95243493",
518
+ "language": "Jupyter",
519
+ "lines": 504,
520
+ "truncated": false,
521
+ "block": 3,
522
+ "row": 7740
523
+ },
524
+ {
525
+ "path": "paper_analyses/fig2_singlecell_multiomics/metrics_bench_plot.ipynb",
526
+ "sha256": "4f41658c33ad8a866a8bec2c3c2569a4d5d2d8f91fc146f6cb41a9f5348ea6e2",
527
+ "language": "Jupyter",
528
+ "lines": 714,
529
+ "truncated": false,
530
+ "block": 3,
531
+ "row": 7822
532
+ },
533
+ {
534
+ "path": "paper_analyses/fig2_singlecell_multiomics/rna_adt/02.Vertical_RNA_ADT_benchmark.ipynb",
535
+ "sha256": "354818b57e73eb936b97b9dc0eb7548f56df4ce5e9547fcedfa6620586b49b18",
536
+ "language": "Jupyter",
537
+ "lines": 1136,
538
+ "truncated": false,
539
+ "block": 3,
540
+ "row": 7815
541
+ },
542
+ {
543
+ "path": "paper_analyses/fig2_singlecell_multiomics/rna_adt/Benchmark_scMulti-omics(RNA+Protein).ipynb",
544
+ "sha256": "f6974c0f36dbaea461ab8c765783488dc69d4440c87b9f2ceb84e654c86e2f1f",
545
+ "language": "Jupyter",
546
+ "lines": 709,
547
+ "truncated": false,
548
+ "block": 3,
549
+ "row": 7764
550
+ }
551
+ ]
552
+ }
manifests/fc/zenodo__21730421.json ADDED
@@ -0,0 +1,264 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:21730421",
4
+ "url": "https://doi.org/10.5281/zenodo.21730421",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "CC-BY-4.0",
8
+ "license_confirmed_by": "license file LICENSE.txt",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE.txt",
13
+ "sha256": "dbf067b02ef91a2638e8ff07e46708e9df60da0ce82c3db35ba68953c24c2a7e",
14
+ "language": "License",
15
+ "lines": 6,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 7900
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "028023918ec02cab3947c86135b0cfe690f278f25f4eb9d60093eae7208d3d4c",
23
+ "language": "Text",
24
+ "lines": 146,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2631
28
+ },
29
+ {
30
+ "path": "code/build_dataset.py",
31
+ "sha256": "7de074eb8fc7c86570949a175838b655928e8ee26403d5a10f13b5af8529eb9f",
32
+ "language": "Python",
33
+ "lines": 291,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 26061
37
+ },
38
+ {
39
+ "path": "code/calibrate_node.py",
40
+ "sha256": "3c670dfd080fd4452ab502131328d504285a03e834255aeca02e0ce940dc3b7e",
41
+ "language": "Python",
42
+ "lines": 213,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 25401
46
+ },
47
+ {
48
+ "path": "code/canal_hibridacao.py",
49
+ "sha256": "180db8afeec7c5423b45b7689cd7f741114e6d2e8320d870b9b909a099db4a7d",
50
+ "language": "Python",
51
+ "lines": 96,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 22484
55
+ },
56
+ {
57
+ "path": "code/confere_referencias.py",
58
+ "sha256": "3bf8952a95fba014bbc5e0f7233660bed0cbe865f990b7f113701246260016fd",
59
+ "language": "Python",
60
+ "lines": 108,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 22310
64
+ },
65
+ {
66
+ "path": "code/controles_r2.py",
67
+ "sha256": "2fc25827fc37425bdb750728857f58db2824feb3470a3150804d504c3df0c986",
68
+ "language": "Python",
69
+ "lines": 109,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 23305
73
+ },
74
+ {
75
+ "path": "code/dos_analise.py",
76
+ "sha256": "6e28dbba5a1ce192ea719b9c06e684e3f22801bbf511b06dca3b80f60f9e0411",
77
+ "language": "Python",
78
+ "lines": 212,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 25499
82
+ },
83
+ {
84
+ "path": "code/dos_analise_final.py",
85
+ "sha256": "17bed1309507cda69fdee29e95d18c3be524d3053294fe2f443022dcbbf6d158",
86
+ "language": "Python",
87
+ "lines": 187,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 25002
91
+ },
92
+ {
93
+ "path": "code/dos_remoto.py",
94
+ "sha256": "36126522a60f2e70583a5c97d747233e83d9adbebdadaef849f18ed67192631a",
95
+ "language": "Python",
96
+ "lines": 169,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 24095
100
+ },
101
+ {
102
+ "path": "code/escassez_grupos.py",
103
+ "sha256": "9a933ae1a3a98f2b83c4d9462f3682da8da47789594ce69907bf3670e3155cee",
104
+ "language": "Python",
105
+ "lines": 148,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 24404
109
+ },
110
+ {
111
+ "path": "code/fig_manuscrito.py",
112
+ "sha256": "ffcad3de65ad6cea29316cc097a2e4dea8d3b157877259c55accd93935294edc",
113
+ "language": "Python",
114
+ "lines": 109,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 23051
118
+ },
119
+ {
120
+ "path": "code/fig_mecanismo.py",
121
+ "sha256": "8fd09df8789495d1ebc3112a1fbccc6938bc68ec0013e974a7e41cd83b53c726",
122
+ "language": "Python",
123
+ "lines": 197,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 25161
127
+ },
128
+ {
129
+ "path": "code/gen_inputs.py",
130
+ "sha256": "f9b2f3c27234963e611479ace7b956ecd2dbfda136cf3f79c92ab7f4be8e5554",
131
+ "language": "Python",
132
+ "lines": 105,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 21961
136
+ },
137
+ {
138
+ "path": "code/groupkfold_interno.py",
139
+ "sha256": "8e3313bb42cee6e4808e068559e163711ad37fd9344c2b8271cf3fa798d82156",
140
+ "language": "Python",
141
+ "lines": 137,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 24046
145
+ },
146
+ {
147
+ "path": "code/magpie_e_curva.py",
148
+ "sha256": "8560ad374d83ecf54572118840e85fe1ae0049497027d9b9b702f6b22d38e749",
149
+ "language": "Python",
150
+ "lines": 151,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 24227
154
+ },
155
+ {
156
+ "path": "code/mkfdf.py",
157
+ "sha256": "705873719f8dc8c2d9cba21981ea16664d896e4582f5d027a175078f30d39cb3",
158
+ "language": "Python",
159
+ "lines": 217,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 24217
163
+ },
164
+ {
165
+ "path": "code/perfil_alpha.py",
166
+ "sha256": "9283a76caf1a99721f81cc1942d63e8f3fa5b055f244ed9d23d81aa9559e2955",
167
+ "language": "Python",
168
+ "lines": 139,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 23962
172
+ },
173
+ {
174
+ "path": "code/postprocess.py",
175
+ "sha256": "e5fed2031747db8fdd070877293eafd26c5b76b067f1e0870b420c0456be8f25",
176
+ "language": "Python",
177
+ "lines": 713,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 27636
181
+ },
182
+ {
183
+ "path": "code/preflight.py",
184
+ "sha256": "597701928bda331ee38d45654c242b4c83a2d309e73b11aae3892d49fe64fb67",
185
+ "language": "Python",
186
+ "lines": 565,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 27406
190
+ },
191
+ {
192
+ "path": "code/run_queue.py",
193
+ "sha256": "bc31ce777d31b22dad1c7cdfb6b0f760a3d905e78bdd6c79a179d18c6ab7a8ea",
194
+ "language": "Python",
195
+ "lines": 405,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 26761
199
+ },
200
+ {
201
+ "path": "code/testa_gap_com_dos.py",
202
+ "sha256": "5a985e6cb70fc7cd39d5c012898517fa6e9bebfb76de1aca658e0a1dc3a2b7d0",
203
+ "language": "Python",
204
+ "lines": 115,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 23406
208
+ },
209
+ {
210
+ "path": "code/testa_hibridacao.py",
211
+ "sha256": "faff6052e98fac0312f12837c14dcd2e1735ddb409397e4ae629985c407a30df",
212
+ "language": "Python",
213
+ "lines": 149,
214
+ "truncated": false,
215
+ "block": 3,
216
+ "row": 24210
217
+ },
218
+ {
219
+ "path": "code/testa_oce_dos.py",
220
+ "sha256": "b4f6942df021bb4efa50c3a0ad61901a68bcd56c86bc81a45fe05ca63cc882a1",
221
+ "language": "Python",
222
+ "lines": 82,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 22364
226
+ },
227
+ {
228
+ "path": "code/testa_ridge_bloco.py",
229
+ "sha256": "3ee7e8e9c19b11eb13905f44f71af5cc81830f20da3d8a8c02e94aa48c72ac27",
230
+ "language": "Python",
231
+ "lines": 148,
232
+ "truncated": false,
233
+ "block": 3,
234
+ "row": 24261
235
+ },
236
+ {
237
+ "path": "code/testa_segunda_derivada_r2.py",
238
+ "sha256": "dfc7b3d0518283e870f000f9c9c52cf695887b739fe8c885a9e83ef6355cf354",
239
+ "language": "Python",
240
+ "lines": 200,
241
+ "truncated": false,
242
+ "block": 3,
243
+ "row": 25180
244
+ },
245
+ {
246
+ "path": "code/variancia_selecao_alpha.py",
247
+ "sha256": "1faae043741fc6392a99a5cfcd683cfd97f15a7b4ece892d497265b378236a10",
248
+ "language": "Python",
249
+ "lines": 107,
250
+ "truncated": false,
251
+ "block": 3,
252
+ "row": 22969
253
+ },
254
+ {
255
+ "path": "code/verifica_alpha_gap.py",
256
+ "sha256": "7cbb7f696c0a27129c8cff32364a2fa719040529a7c58815bd2e3775452f2d94",
257
+ "language": "Python",
258
+ "lines": 75,
259
+ "truncated": false,
260
+ "block": 3,
261
+ "row": 22159
262
+ }
263
+ ]
264
+ }
manifests/fd/github.com__nagellab__mayetal2026.json ADDED
The diff for this file is too large to render. See raw diff
 
manifests/fe/github.com__scverse__scvi-tools.json ADDED
@@ -0,0 +1,3072 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/scverse/scvi-tools",
4
+ "url": "https://github.com/scverse/scvi-tools",
5
+ "host": "github.com",
6
+ "commit": "fa9470f9b59f47a1df1677eda44161ac14845db3",
7
+ "license": "BSD-3-Clause",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "66399db0284d2539790efb348886ab0c1f745bbe5fea6ac38a00465a14adc8f5",
14
+ "language": "License",
15
+ "lines": 30,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8127
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "eb46b8a54e60643ca0cd8cb375ede05b01dcbd2380ca17ce8027a92ba13cebbb",
23
+ "language": "Text",
24
+ "lines": 147,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2590
28
+ },
29
+ {
30
+ "path": "conftest.py",
31
+ "sha256": "42c3f1717ba4d6bd434dd9be5197ee5a12c3f3e5be7629e8f62979dfb4c8a4c7",
32
+ "language": "Python",
33
+ "lines": 62,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 19911
37
+ },
38
+ {
39
+ "path": "docs/_static/js/custom.js",
40
+ "sha256": "b0486605fbef3e68b050c2d1d2450b96abb21ea7d6cc6c72cf42fe383237a188",
41
+ "language": "JavaScript",
42
+ "lines": 164,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 6907
46
+ },
47
+ {
48
+ "path": "docs/conf.py",
49
+ "sha256": "3a9853a519b73065ff96e715e3d025d39a79f7b65fa79a7bbb73e0e640c0805c",
50
+ "language": "Python",
51
+ "lines": 343,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 25729
55
+ },
56
+ {
57
+ "path": "docs/extensions/edit_colab_url.py",
58
+ "sha256": "4f9b3be99f445bfb2203d6e6a9ba2bac7bf781382c730e488927efefd4975d3c",
59
+ "language": "Python",
60
+ "lines": 39,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 19401
64
+ },
65
+ {
66
+ "path": "docs/extensions/filterlist.py",
67
+ "sha256": "7d0ed39f2b23f4f90d01377fa8dad304a1eb5c77caf52cd8c6ebd3b02bb25bef",
68
+ "language": "Python",
69
+ "lines": 319,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 25053
73
+ },
74
+ {
75
+ "path": "docs/extensions/typed_returns.py",
76
+ "sha256": "ff0b557517ae5ec71c038fd7d921dc73d38a707defeb796fe10d5b54c61c9ee2",
77
+ "language": "Python",
78
+ "lines": 35,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 19078
82
+ },
83
+ {
84
+ "path": "src/scvi/__init__.py",
85
+ "sha256": "9ce050b96db979e9955bb139ea136986780398dc3c4794227e59347f11e41255",
86
+ "language": "Python",
87
+ "lines": 31,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 18552
91
+ },
92
+ {
93
+ "path": "src/scvi/_constants.py",
94
+ "sha256": "a794aa0a9dda827a1306567166da372b2466ef8f7ff395e7ada01e4e89d93099",
95
+ "language": "Python",
96
+ "lines": 21,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 18521
100
+ },
101
+ {
102
+ "path": "src/scvi/_settings.py",
103
+ "sha256": "b78e0a9db61cec067e1acce551e2012401388b9dd2041779be34d749fb567ca0",
104
+ "language": "Python",
105
+ "lines": 231,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 24260
109
+ },
110
+ {
111
+ "path": "src/scvi/_types.py",
112
+ "sha256": "6d5452cca31b5e652ae92b91fa509925d83c489f92fc10bab6c442e00f116a28",
113
+ "language": "Python",
114
+ "lines": 13,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 17853
118
+ },
119
+ {
120
+ "path": "src/scvi/autotune/__init__.py",
121
+ "sha256": "64d7641e9e7371331fe33405e2c8c112daf12d59bd760bb23292ad642520f0fc",
122
+ "language": "Python",
123
+ "lines": 34,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 19296
127
+ },
128
+ {
129
+ "path": "src/scvi/autotune/_experiment.py",
130
+ "sha256": "ad34350f5f2d346f074d438bf96d9401246c16dcc150817f662d2a738204fa13",
131
+ "language": "Python",
132
+ "lines": 896,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 27773
136
+ },
137
+ {
138
+ "path": "src/scvi/autotune/_tune.py",
139
+ "sha256": "7b1f4f69c312723f0809d1d5ec68724077d6d0be65706b56c8ca1128ca4518fa",
140
+ "language": "Python",
141
+ "lines": 181,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 24105
145
+ },
146
+ {
147
+ "path": "src/scvi/criticism/__init__.py",
148
+ "sha256": "54668d23e0b44167c9023d4452d0974903f9578559733f8cc8102ae58fbed635",
149
+ "language": "Python",
150
+ "lines": 4,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 17659
154
+ },
155
+ {
156
+ "path": "src/scvi/criticism/_constants.py",
157
+ "sha256": "62c3a843a41dc45eb5627d8162f09a4b637188a20bc445e251808a1ead3a2879",
158
+ "language": "Python",
159
+ "lines": 14,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 18122
163
+ },
164
+ {
165
+ "path": "src/scvi/criticism/_create_criticism_report.py",
166
+ "sha256": "3daf8a4975eccbf9289686f7d335729134e888ceda2c06fd022f39d2f86a2582",
167
+ "language": "Python",
168
+ "lines": 226,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 24801
172
+ },
173
+ {
174
+ "path": "src/scvi/criticism/_ppc.py",
175
+ "sha256": "8cdff0aae1e35a4a729f12bd95159881fe972c3a188b483a288880696d84eff7",
176
+ "language": "Python",
177
+ "lines": 481,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 27029
181
+ },
182
+ {
183
+ "path": "src/scvi/data/__init__.py",
184
+ "sha256": "18a41c7955454603303f5a9e5643cab13a1716b990a5d9cf4577284d7a1632ac",
185
+ "language": "Python",
186
+ "lines": 68,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 19731
190
+ },
191
+ {
192
+ "path": "src/scvi/data/_anntorchdataset.py",
193
+ "sha256": "69632487e687641873aa857182d9b0008e2eb23f006f891fc93de47380db5e32",
194
+ "language": "Python",
195
+ "lines": 169,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 23802
199
+ },
200
+ {
201
+ "path": "src/scvi/data/_built_in_data/_brain_large.py",
202
+ "sha256": "dc33207b6878dda0d5bb543875fcbfdbaeb7ea1af62bdd3bae5dd9c06bfb0a7a",
203
+ "language": "Python",
204
+ "lines": 112,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 22333
208
+ },
209
+ {
210
+ "path": "src/scvi/data/_built_in_data/_cellxgene.py",
211
+ "sha256": "11052400b087d233106872adfa8b63d135ed0d409b3a3acc6d0bc60bc4a9b8ea",
212
+ "language": "Python",
213
+ "lines": 62,
214
+ "truncated": false,
215
+ "block": 3,
216
+ "row": 19685
217
+ },
218
+ {
219
+ "path": "src/scvi/data/_built_in_data/_cite_seq.py",
220
+ "sha256": "6991bae25ee84a24e106fbd45af1c084735fd96fac0b3fa405c6cc05ef99a8d9",
221
+ "language": "Python",
222
+ "lines": 187,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 24067
226
+ },
227
+ {
228
+ "path": "src/scvi/data/_built_in_data/_cortex.py",
229
+ "sha256": "adaf058e8b8f1e49a632da60d81e6c786e35e632b5c193ada123bc58a80de25f",
230
+ "language": "Python",
231
+ "lines": 58,
232
+ "truncated": false,
233
+ "block": 3,
234
+ "row": 20075
235
+ },
236
+ {
237
+ "path": "src/scvi/data/_built_in_data/_csv.py",
238
+ "sha256": "39df0493b99aed8e3442b90a7c0d809c29de8b225b4200c9fb6aaabd5d89568b",
239
+ "language": "Python",
240
+ "lines": 49,
241
+ "truncated": false,
242
+ "block": 3,
243
+ "row": 19642
244
+ },
245
+ {
246
+ "path": "src/scvi/data/_built_in_data/_dataset_10x.py",
247
+ "sha256": "86229a33e5c00f4f654bb7692f3ee6880468f18c35db82403adad098c2f49767",
248
+ "language": "Python",
249
+ "lines": 171,
250
+ "truncated": false,
251
+ "block": 3,
252
+ "row": 23520
253
+ },
254
+ {
255
+ "path": "src/scvi/data/_built_in_data/_heartcellatlas.py",
256
+ "sha256": "3b2732af12fa3405fb63025f0ecafa27a1b8362d746aefcd7a78008b20fe9160",
257
+ "language": "Python",
258
+ "lines": 47,
259
+ "truncated": false,
260
+ "block": 3,
261
+ "row": 19474
262
+ },
263
+ {
264
+ "path": "src/scvi/data/_built_in_data/_loom.py",
265
+ "sha256": "8898b45dd75ba3d7f2254aef92c9de4fc99c692f73a1fad00b5326723ecff36a",
266
+ "language": "Python",
267
+ "lines": 103,
268
+ "truncated": false,
269
+ "block": 3,
270
+ "row": 21691
271
+ },
272
+ {
273
+ "path": "src/scvi/data/_built_in_data/_pbmc.py",
274
+ "sha256": "fb0b6801c9188980d60dd63676917bb7549ef6e57f397af7b7d50e2dfa27040f",
275
+ "language": "Python",
276
+ "lines": 121,
277
+ "truncated": false,
278
+ "block": 3,
279
+ "row": 22431
280
+ },
281
+ {
282
+ "path": "src/scvi/data/_built_in_data/_smfish.py",
283
+ "sha256": "aa5a70a55e61acb2cf650f10a4d14bf09e72459e5196327b2a796a390bb33577",
284
+ "language": "Python",
285
+ "lines": 81,
286
+ "truncated": false,
287
+ "block": 3,
288
+ "row": 20825
289
+ },
290
+ {
291
+ "path": "src/scvi/data/_built_in_data/_synthetic.py",
292
+ "sha256": "5748d6fbf799d511c540c200d7c3d9ed2ba46bb92c514ff6270f99b5ed8d372c",
293
+ "language": "Python",
294
+ "lines": 113,
295
+ "truncated": false,
296
+ "block": 3,
297
+ "row": 21853
298
+ },
299
+ {
300
+ "path": "src/scvi/data/_compat.py",
301
+ "sha256": "f4869cb217437695d244818e5efd56158036d8c586c2c111f85595b54c47129e",
302
+ "language": "Python",
303
+ "lines": 173,
304
+ "truncated": false,
305
+ "block": 3,
306
+ "row": 24450
307
+ },
308
+ {
309
+ "path": "src/scvi/data/_constants.py",
310
+ "sha256": "4f3b4d3a015b997deabd3a62867fff30510c1b2e02968405df60cfa1176d1f48",
311
+ "language": "Python",
312
+ "lines": 60,
313
+ "truncated": false,
314
+ "block": 3,
315
+ "row": 19557
316
+ },
317
+ {
318
+ "path": "src/scvi/data/_datasets.py",
319
+ "sha256": "e8e97b3c663622afb6ca271ba2cff3c4114faf018e1bcc5431ca26919f2021d3",
320
+ "language": "Python",
321
+ "lines": 698,
322
+ "truncated": false,
323
+ "block": 3,
324
+ "row": 27209
325
+ },
326
+ {
327
+ "path": "src/scvi/data/_download.py",
328
+ "sha256": "7a5f0d73210d1d76c3e508aaa9f647c54292d000ba794a16c7968d93c7941082",
329
+ "language": "Python",
330
+ "lines": 116,
331
+ "truncated": false,
332
+ "block": 3,
333
+ "row": 22545
334
+ },
335
+ {
336
+ "path": "src/scvi/data/_manager.py",
337
+ "sha256": "4c6f4a0d37a34d53968f012c5078598d4c7ca36b932c9b103f8f7cd1222b3719",
338
+ "language": "Python",
339
+ "lines": 570,
340
+ "truncated": false,
341
+ "block": 3,
342
+ "row": 27153
343
+ },
344
+ {
345
+ "path": "src/scvi/data/_preprocessing.py",
346
+ "sha256": "ded42fd69131949b818ee185d976a773829b53487581cc53682d4bac95a42b83",
347
+ "language": "Python",
348
+ "lines": 492,
349
+ "truncated": false,
350
+ "block": 3,
351
+ "row": 26845
352
+ },
353
+ {
354
+ "path": "src/scvi/data/_read.py",
355
+ "sha256": "957e12c4a91e63bbc91be5304e5e254cd1488c6839d9d79ba8748124bff183bd",
356
+ "language": "Python",
357
+ "lines": 71,
358
+ "truncated": false,
359
+ "block": 3,
360
+ "row": 20404
361
+ },
362
+ {
363
+ "path": "src/scvi/data/_utils.py",
364
+ "sha256": "2f64c72a2191986586edbb62487fcff23c39076dde4e6d41ed414b164944e4ad",
365
+ "language": "Python",
366
+ "lines": 383,
367
+ "truncated": false,
368
+ "block": 3,
369
+ "row": 26119
370
+ },
371
+ {
372
+ "path": "src/scvi/data/fields/__init__.py",
373
+ "sha256": "cf49a5a24a3ad2e2520b60406db7d5724824708009c6f0260c96b9ff09492dd1",
374
+ "language": "Python",
375
+ "lines": 64,
376
+ "truncated": false,
377
+ "block": 3,
378
+ "row": 19999
379
+ },
380
+ {
381
+ "path": "src/scvi/data/fields/_arraylike_field.py",
382
+ "sha256": "d60b957d9fc7b72a9de291df9c032e933ca1f038e05b57e18a7ada512888210c",
383
+ "language": "Python",
384
+ "lines": 522,
385
+ "truncated": false,
386
+ "block": 3,
387
+ "row": 26902
388
+ },
389
+ {
390
+ "path": "src/scvi/data/fields/_base_field.py",
391
+ "sha256": "5144bae6053bc6e7db2399e924e022311ca62516361d819779c30defa07a7225",
392
+ "language": "Python",
393
+ "lines": 151,
394
+ "truncated": false,
395
+ "block": 3,
396
+ "row": 23257
397
+ },
398
+ {
399
+ "path": "src/scvi/data/fields/_dataframe_field.py",
400
+ "sha256": "f815ff8b35a0de2a4d24bc6e2412f157632ba2b0e000b9e7c34c7da241e1dec3",
401
+ "language": "Python",
402
+ "lines": 293,
403
+ "truncated": false,
404
+ "block": 3,
405
+ "row": 25393
406
+ },
407
+ {
408
+ "path": "src/scvi/data/fields/_layer_field.py",
409
+ "sha256": "3b0b9204b8751781970b7f7a33f21b6e1654b662c69fbd8b8dd737e5223e3255",
410
+ "language": "Python",
411
+ "lines": 147,
412
+ "truncated": false,
413
+ "block": 3,
414
+ "row": 23011
415
+ },
416
+ {
417
+ "path": "src/scvi/data/fields/_mudata.py",
418
+ "sha256": "63366ce5e1dbe10f20b66eb7ff1f65b52f5a985216d881ebf0339d9f751b1bc5",
419
+ "language": "Python",
420
+ "lines": 143,
421
+ "truncated": false,
422
+ "block": 3,
423
+ "row": 23217
424
+ },
425
+ {
426
+ "path": "src/scvi/data/fields/_protein.py",
427
+ "sha256": "7a2f5fe70701526cdbdc5cc48944626050c59ffe7e108fd7eb3a37ce0fd1dbc3",
428
+ "language": "Python",
429
+ "lines": 165,
430
+ "truncated": false,
431
+ "block": 3,
432
+ "row": 23781
433
+ },
434
+ {
435
+ "path": "src/scvi/data/fields/_scanvi.py",
436
+ "sha256": "5e76b2d37ec785e10145a77a18bd085324479442bded599871d193d55179d1cd",
437
+ "language": "Python",
438
+ "lines": 113,
439
+ "truncated": false,
440
+ "block": 3,
441
+ "row": 22239
442
+ },
443
+ {
444
+ "path": "src/scvi/data/fields/_uns_field.py",
445
+ "sha256": "6bb10f62b0f077d264fce028b279171af8953a05e65db175107589a968bb773e",
446
+ "language": "Python",
447
+ "lines": 84,
448
+ "truncated": false,
449
+ "block": 3,
450
+ "row": 20672
451
+ },
452
+ {
453
+ "path": "src/scvi/dataloaders/__init__.py",
454
+ "sha256": "e2490901d38633f7d1907f003eff84e54880ba1eb79e72ca6435226bddc2d4ba",
455
+ "language": "Python",
456
+ "lines": 33,
457
+ "truncated": false,
458
+ "block": 3,
459
+ "row": 18878
460
+ },
461
+ {
462
+ "path": "src/scvi/dataloaders/_ann_dataloader.py",
463
+ "sha256": "8c9ad1bbb4cf37676e8a055d8750772348efefebbdf91c6b1fc948eed938345a",
464
+ "language": "Python",
465
+ "lines": 138,
466
+ "truncated": false,
467
+ "block": 3,
468
+ "row": 23493
469
+ },
470
+ {
471
+ "path": "src/scvi/dataloaders/_anncollection.py",
472
+ "sha256": "f55cd5a589d0ded1f7993d12834ff804de19fdab21310775e5e9b0f158b78d6e",
473
+ "language": "Python",
474
+ "lines": 120,
475
+ "truncated": false,
476
+ "block": 3,
477
+ "row": 21828
478
+ },
479
+ {
480
+ "path": "src/scvi/dataloaders/_concat_dataloader.py",
481
+ "sha256": "b455698bee99d2764e6c74c8f8ba73c1b54a9e2b3d4d8c52cfe9cf7fd8556bf0",
482
+ "language": "Python",
483
+ "lines": 95,
484
+ "truncated": false,
485
+ "block": 3,
486
+ "row": 21809
487
+ },
488
+ {
489
+ "path": "src/scvi/dataloaders/_custom_dataloaders.py",
490
+ "sha256": "5bd41a023831d1d3d0d9773358674a4b5cb16a29a9fda31aaacfd6b342b7606a",
491
+ "language": "Python",
492
+ "lines": 1521,
493
+ "truncated": false,
494
+ "block": 3,
495
+ "row": 28026
496
+ },
497
+ {
498
+ "path": "src/scvi/dataloaders/_data_splitting.py",
499
+ "sha256": "0004e4915f82ac2f550981501b77b13a2a77ac93a9fc6f15970b51253a711e09",
500
+ "language": "Python",
501
+ "lines": 771,
502
+ "truncated": false,
503
+ "block": 3,
504
+ "row": 27605
505
+ },
506
+ {
507
+ "path": "src/scvi/dataloaders/_samplers.py",
508
+ "sha256": "0abac9473b2d61062b3f7c6e473081e5f5a107fbafacd326c3494b80a66f0903",
509
+ "language": "Python",
510
+ "lines": 89,
511
+ "truncated": false,
512
+ "block": 3,
513
+ "row": 21778
514
+ },
515
+ {
516
+ "path": "src/scvi/dataloaders/_semi_dataloader.py",
517
+ "sha256": "743008b175340fa98ae77d2a0f7cf578faaad9e34e23b22fd4649ab01843f9ce",
518
+ "language": "Python",
519
+ "lines": 114,
520
+ "truncated": false,
521
+ "block": 3,
522
+ "row": 22380
523
+ },
524
+ {
525
+ "path": "src/scvi/distributions/__init__.py",
526
+ "sha256": "0815e91a5f7b8357872d31f16f8732c7361ef4a054f3b3f0829fa7ce4da03b0e",
527
+ "language": "Python",
528
+ "lines": 24,
529
+ "truncated": false,
530
+ "block": 3,
531
+ "row": 18468
532
+ },
533
+ {
534
+ "path": "src/scvi/distributions/_beta_binomial.py",
535
+ "sha256": "2fccdbddb60030906155f26fc6ac58a0ae8f91cd6a1e08faf42eea44e12efd76",
536
+ "language": "Python",
537
+ "lines": 153,
538
+ "truncated": false,
539
+ "block": 3,
540
+ "row": 23453
541
+ },
542
+ {
543
+ "path": "src/scvi/distributions/_constraints.py",
544
+ "sha256": "200ec0b3a0f67a1a0d30516cee53f1e9e6b4174897e73ba256d0134941d7311a",
545
+ "language": "Python",
546
+ "lines": 41,
547
+ "truncated": false,
548
+ "block": 3,
549
+ "row": 19267
550
+ },
551
+ {
552
+ "path": "src/scvi/distributions/_gamma.py",
553
+ "sha256": "bfb55648ac422a8a4a3dd5fa45f90b85834a60e77724297d80f158da6935e20a",
554
+ "language": "Python",
555
+ "lines": 201,
556
+ "truncated": false,
557
+ "block": 3,
558
+ "row": 23963
559
+ },
560
+ {
561
+ "path": "src/scvi/distributions/_lognormal.py",
562
+ "sha256": "4170dce01978ab1daaf0f735d32bc96314440538daf21b54348e7178bf8affe2",
563
+ "language": "Python",
564
+ "lines": 316,
565
+ "truncated": false,
566
+ "block": 3,
567
+ "row": 25604
568
+ },
569
+ {
570
+ "path": "src/scvi/distributions/_negative_binomial.py",
571
+ "sha256": "80e1008fea621617f76d332f3646732592f6efd86b91b6136ba125d3067f6da7",
572
+ "language": "Python",
573
+ "lines": 724,
574
+ "truncated": false,
575
+ "block": 3,
576
+ "row": 27272
577
+ },
578
+ {
579
+ "path": "src/scvi/distributions/_normal.py",
580
+ "sha256": "5690da9e5b40501c959602e1d59f999bd6a85df11ab8020674ff824b57da6178",
581
+ "language": "Python",
582
+ "lines": 57,
583
+ "truncated": false,
584
+ "block": 3,
585
+ "row": 19686
586
+ },
587
+ {
588
+ "path": "src/scvi/distributions/_utils.py",
589
+ "sha256": "37c341dc41c11ebc5d8b0c3d3ab203ed80ca040861cf735d27c97c28f68a9c8f",
590
+ "language": "Python",
591
+ "lines": 94,
592
+ "truncated": false,
593
+ "block": 3,
594
+ "row": 21700
595
+ },
596
+ {
597
+ "path": "src/scvi/external/__init__.py",
598
+ "sha256": "fa64e068cc033f0617e5aa36bffdaf1a9736dd4238f640407dedb101e84f12ed",
599
+ "language": "Python",
600
+ "lines": 50,
601
+ "truncated": false,
602
+ "block": 3,
603
+ "row": 19143
604
+ },
605
+ {
606
+ "path": "src/scvi/external/cellassign/__init__.py",
607
+ "sha256": "a0d4225476b4d607d51695f3abcb8f500722f6de9c00909c75e78275a5b80515",
608
+ "language": "Python",
609
+ "lines": 4,
610
+ "truncated": false,
611
+ "block": 3,
612
+ "row": 17562
613
+ },
614
+ {
615
+ "path": "src/scvi/external/cellassign/_model.py",
616
+ "sha256": "ee7487865759c15a0bc180ad3e86ca43f94e4cd57ead3de01378275b38229738",
617
+ "language": "Python",
618
+ "lines": 294,
619
+ "truncated": false,
620
+ "block": 3,
621
+ "row": 25652
622
+ },
623
+ {
624
+ "path": "src/scvi/external/cellassign/_module.py",
625
+ "sha256": "44cbacc0f77a0e1132bb6e6a6776e58f7a64698ab1cf322f688b7282d0abe1dc",
626
+ "language": "Python",
627
+ "lines": 265,
628
+ "truncated": false,
629
+ "block": 3,
630
+ "row": 25175
631
+ },
632
+ {
633
+ "path": "src/scvi/external/contrastivevi/__init__.py",
634
+ "sha256": "36da1fbd145454ff5fd5ff006fd851b21a9981c483a6efb72b27e2c7c406d289",
635
+ "language": "Python",
636
+ "lines": 11,
637
+ "truncated": false,
638
+ "block": 3,
639
+ "row": 17879
640
+ },
641
+ {
642
+ "path": "src/scvi/external/contrastivevi/_contrastive_data_splitting.py",
643
+ "sha256": "e5c050ca5bbf40c6bccde806a8ef0ab332f19a141d925d0a7a098306760a9f45",
644
+ "language": "Python",
645
+ "lines": 218,
646
+ "truncated": false,
647
+ "block": 3,
648
+ "row": 25111
649
+ },
650
+ {
651
+ "path": "src/scvi/external/contrastivevi/_contrastive_dataloader.py",
652
+ "sha256": "9cbf47d2237bf05572eaf0f956b19808d054593f4a47b91eb6d3bae35317fdf3",
653
+ "language": "Python",
654
+ "lines": 123,
655
+ "truncated": false,
656
+ "block": 3,
657
+ "row": 22831
658
+ },
659
+ {
660
+ "path": "src/scvi/external/contrastivevi/_model.py",
661
+ "sha256": "63e7ca90841e9bf0ab5fabfa1b223d703231f0c4c8ffee41d923128e02aa4367",
662
+ "language": "Python",
663
+ "lines": 860,
664
+ "truncated": false,
665
+ "block": 3,
666
+ "row": 27746
667
+ },
668
+ {
669
+ "path": "src/scvi/external/contrastivevi/_module.py",
670
+ "sha256": "aaf051051cb26a3394c9c695896b44fcbb8f4c4d257e12a86115f864b90dfbef",
671
+ "language": "Python",
672
+ "lines": 610,
673
+ "truncated": false,
674
+ "block": 3,
675
+ "row": 27278
676
+ },
677
+ {
678
+ "path": "src/scvi/external/cytovi/__init__.py",
679
+ "sha256": "b5f1ec60aca1ff058ecd91bcdedd33696c5239900b5af3e85bb4a3df33860d09",
680
+ "language": "Python",
681
+ "lines": 15,
682
+ "truncated": false,
683
+ "block": 3,
684
+ "row": 18207
685
+ },
686
+ {
687
+ "path": "src/scvi/external/cytovi/_constants.py",
688
+ "sha256": "aee147dfa11a620fee2a4171c38a77fe7ab0f2d06b37c7278b1b8c6dce98c759",
689
+ "language": "Python",
690
+ "lines": 22,
691
+ "truncated": false,
692
+ "block": 3,
693
+ "row": 18580
694
+ },
695
+ {
696
+ "path": "src/scvi/external/cytovi/_model.py",
697
+ "sha256": "46b9f49c099cb43e1b6755db16cfa32683ea391cd63b488048abeec64fc44158",
698
+ "language": "Python",
699
+ "lines": 1241,
700
+ "truncated": false,
701
+ "block": 3,
702
+ "row": 27938
703
+ },
704
+ {
705
+ "path": "src/scvi/external/cytovi/_module.py",
706
+ "sha256": "2271abcdb512d4624808832add8ffbeb0870702c9b3f72036b489c04309218b9",
707
+ "language": "Python",
708
+ "lines": 576,
709
+ "truncated": false,
710
+ "block": 3,
711
+ "row": 27105
712
+ },
713
+ {
714
+ "path": "src/scvi/external/cytovi/_plotting.py",
715
+ "sha256": "326de16211fb929fa462d6d7507a90df411cb12a520de2ecc85caddf7ee8942d",
716
+ "language": "Python",
717
+ "lines": 268,
718
+ "truncated": false,
719
+ "block": 3,
720
+ "row": 24639
721
+ },
722
+ {
723
+ "path": "src/scvi/external/cytovi/_preprocessing.py",
724
+ "sha256": "eccde33514cd08b0331da7a818f6ba21e6c3323b10bde6fec3c04ad8a2a56598",
725
+ "language": "Python",
726
+ "lines": 408,
727
+ "truncated": false,
728
+ "block": 3,
729
+ "row": 26315
730
+ },
731
+ {
732
+ "path": "src/scvi/external/cytovi/_read_write.py",
733
+ "sha256": "5d20b91b872da434b59ae85efbf0d9c232f5ceebc02f4db5675a7fa6b90dbbb6",
734
+ "language": "Python",
735
+ "lines": 270,
736
+ "truncated": false,
737
+ "block": 3,
738
+ "row": 25085
739
+ },
740
+ {
741
+ "path": "src/scvi/external/cytovi/_utils.py",
742
+ "sha256": "8662f5e58629958443bfc790d47938674584d0c10e22f1617d8e40693938bf32",
743
+ "language": "Python",
744
+ "lines": 229,
745
+ "truncated": false,
746
+ "block": 3,
747
+ "row": 24398
748
+ },
749
+ {
750
+ "path": "src/scvi/external/decipher/__init__.py",
751
+ "sha256": "c72122142bd5f1085b4d266748c4a11ae54e4571cabc2cc08a0fb8f8560214da",
752
+ "language": "Python",
753
+ "lines": 4,
754
+ "truncated": false,
755
+ "block": 3,
756
+ "row": 17564
757
+ },
758
+ {
759
+ "path": "src/scvi/external/decipher/_components.py",
760
+ "sha256": "7ffec0ae9b14806ced129ec5ecb99bfb0b23f44246a2c437d8e30168a409c995",
761
+ "language": "Python",
762
+ "lines": 99,
763
+ "truncated": false,
764
+ "block": 3,
765
+ "row": 21792
766
+ },
767
+ {
768
+ "path": "src/scvi/external/decipher/_model.py",
769
+ "sha256": "5f6c6f1019dc3c65a038a6933a4f5394c6fd868a1a55db6144cd3d7724abca7b",
770
+ "language": "Python",
771
+ "lines": 360,
772
+ "truncated": false,
773
+ "block": 3,
774
+ "row": 26104
775
+ },
776
+ {
777
+ "path": "src/scvi/external/decipher/_module.py",
778
+ "sha256": "867b8e6894af2125b579e8934b26489aab50cc81c8715746bda8444555cf5d3d",
779
+ "language": "Python",
780
+ "lines": 183,
781
+ "truncated": false,
782
+ "block": 3,
783
+ "row": 23798
784
+ },
785
+ {
786
+ "path": "src/scvi/external/decipher/_trainingplan.py",
787
+ "sha256": "0655fb6bfdf0f0193194caedcf140663cb359f2a89adb1ceeea35f12850f7221",
788
+ "language": "Python",
789
+ "lines": 143,
790
+ "truncated": false,
791
+ "block": 3,
792
+ "row": 23201
793
+ },
794
+ {
795
+ "path": "src/scvi/external/decipher/utils/__init__.py",
796
+ "sha256": "529ccf28fb1537a43e28fb60f067e2c86acee06a8dcefe2aa3ba32ed96f56709",
797
+ "language": "Python",
798
+ "lines": 4,
799
+ "truncated": false,
800
+ "block": 3,
801
+ "row": 17617
802
+ },
803
+ {
804
+ "path": "src/scvi/external/decipher/utils/_rotate.py",
805
+ "sha256": "4ad9db2e62c45c715609a9bb5d0a1305a611034b7e6b73c7afe940b5726506a5",
806
+ "language": "Python",
807
+ "lines": 109,
808
+ "truncated": false,
809
+ "block": 3,
810
+ "row": 22561
811
+ },
812
+ {
813
+ "path": "src/scvi/external/decipher/utils/_trajectory.py",
814
+ "sha256": "9b158f834dd3e7f031e92972d748affced2269af08f836a2a1c38b4aa8d1ad65",
815
+ "language": "Python",
816
+ "lines": 138,
817
+ "truncated": false,
818
+ "block": 3,
819
+ "row": 22700
820
+ },
821
+ {
822
+ "path": "src/scvi/external/diagvi/__init__.py",
823
+ "sha256": "5ae41ac5162cda2b1552572979b5db76904c24cc184641a4bebb8314504eade3",
824
+ "language": "Python",
825
+ "lines": 7,
826
+ "truncated": false,
827
+ "block": 3,
828
+ "row": 17721
829
+ },
830
+ {
831
+ "path": "src/scvi/external/diagvi/_base_components.py",
832
+ "sha256": "593661523b1c309f26cffa297c78f37cebfca837b807c0c1c4cab72903eacbdf",
833
+ "language": "Python",
834
+ "lines": 270,
835
+ "truncated": false,
836
+ "block": 3,
837
+ "row": 24996
838
+ },
839
+ {
840
+ "path": "src/scvi/external/diagvi/_model.py",
841
+ "sha256": "7a98528e12e01d36031beb3b2af3ac3ad4b6ec7831f8996f3a6a6b39f73e622f",
842
+ "language": "Python",
843
+ "lines": 1245,
844
+ "truncated": false,
845
+ "block": 3,
846
+ "row": 27946
847
+ },
848
+ {
849
+ "path": "src/scvi/external/diagvi/_module.py",
850
+ "sha256": "6646f700a45166d0ccfa87a72af594a5a47a48871ba902b22777808712baf82f",
851
+ "language": "Python",
852
+ "lines": 597,
853
+ "truncated": false,
854
+ "block": 3,
855
+ "row": 27164
856
+ },
857
+ {
858
+ "path": "src/scvi/external/diagvi/_task.py",
859
+ "sha256": "9ee820616a3a634d46abdae7c92a943b0b5a738076bd492cf489f117c4f2b155",
860
+ "language": "Python",
861
+ "lines": 525,
862
+ "truncated": false,
863
+ "block": 3,
864
+ "row": 26824
865
+ },
866
+ {
867
+ "path": "src/scvi/external/diagvi/_utils.py",
868
+ "sha256": "68d136265db251c5504c5ae2f6f7110de9d5a2435368eebfb2373a96e3747f08",
869
+ "language": "Python",
870
+ "lines": 384,
871
+ "truncated": false,
872
+ "block": 3,
873
+ "row": 25981
874
+ },
875
+ {
876
+ "path": "src/scvi/external/drvi/__init__.py",
877
+ "sha256": "12e0e1f2324115aefeb1176055ba0d7dbd20ac9102c9dc787e0aafc4620adf58",
878
+ "language": "Python",
879
+ "lines": 14,
880
+ "truncated": false,
881
+ "block": 3,
882
+ "row": 18243
883
+ },
884
+ {
885
+ "path": "src/scvi/external/drvi/_base_components.py",
886
+ "sha256": "5c1d41390002bf17da2067053d6f5b7bae65ae0afb58273d9e95efa04f02e40d",
887
+ "language": "Python",
888
+ "lines": 313,
889
+ "truncated": false,
890
+ "block": 3,
891
+ "row": 26438
892
+ },
893
+ {
894
+ "path": "src/scvi/external/drvi/_constants.py",
895
+ "sha256": "9d65ee19cb67ca9921bfa58dd9cd3ccc047df25329eee3aa01be74f520949fba",
896
+ "language": "Python",
897
+ "lines": 10,
898
+ "truncated": false,
899
+ "block": 3,
900
+ "row": 18081
901
+ },
902
+ {
903
+ "path": "src/scvi/external/drvi/_distributions.py",
904
+ "sha256": "6f45abb0281e1c37748be26d63a1d4dae1f7ec0329cf19f7bf09ac7924d2b55f",
905
+ "language": "Python",
906
+ "lines": 132,
907
+ "truncated": false,
908
+ "block": 3,
909
+ "row": 23238
910
+ },
911
+ {
912
+ "path": "src/scvi/external/drvi/_generative_mixin.py",
913
+ "sha256": "1c15ce5f80b563ce1609be4b9432a749a49e7926a592e0ad15767f8757d8e977",
914
+ "language": "Python",
915
+ "lines": 156,
916
+ "truncated": false,
917
+ "block": 3,
918
+ "row": 23789
919
+ },
920
+ {
921
+ "path": "src/scvi/external/drvi/_interpretability_mixin.py",
922
+ "sha256": "3fe1466bf74c2020fd04b2d1bbe19b82c89e2172e58c9855e880e19bf91bd5cb",
923
+ "language": "Python",
924
+ "lines": 722,
925
+ "truncated": false,
926
+ "block": 3,
927
+ "row": 27689
928
+ },
929
+ {
930
+ "path": "src/scvi/external/drvi/_model.py",
931
+ "sha256": "430cef2cd5348d0c21b3d335627749aebcca5e9130da2bff40b24d5595f73996",
932
+ "language": "Python",
933
+ "lines": 109,
934
+ "truncated": false,
935
+ "block": 3,
936
+ "row": 22793
937
+ },
938
+ {
939
+ "path": "src/scvi/external/drvi/_module.py",
940
+ "sha256": "8a60602ea27fe2c4056f80de226b7231640db00a8f6aea17be27d366556b3604",
941
+ "language": "Python",
942
+ "lines": 348,
943
+ "truncated": false,
944
+ "block": 3,
945
+ "row": 26590
946
+ },
947
+ {
948
+ "path": "src/scvi/external/drvi/_trainingplan.py",
949
+ "sha256": "1018467317e43562da6a7d3145d3dc852b8531d8f2221c7e277dc05be0c3d7b6",
950
+ "language": "Python",
951
+ "lines": 48,
952
+ "truncated": false,
953
+ "block": 3,
954
+ "row": 20144
955
+ },
956
+ {
957
+ "path": "src/scvi/external/drvi/_utils.py",
958
+ "sha256": "c477f66b742490f0cb148800723939f7a4bd3411694ff9293bf5f9e885b9ade3",
959
+ "language": "Python",
960
+ "lines": 244,
961
+ "truncated": false,
962
+ "block": 3,
963
+ "row": 25032
964
+ },
965
+ {
966
+ "path": "src/scvi/external/gimvi/__init__.py",
967
+ "sha256": "aff8229ea3f067884060c54f6a6be8e15d3620018ac6fee91e5a53085fc6754d",
968
+ "language": "Python",
969
+ "lines": 4,
970
+ "truncated": false,
971
+ "block": 3,
972
+ "row": 17486
973
+ },
974
+ {
975
+ "path": "src/scvi/external/gimvi/_model.py",
976
+ "sha256": "793645c399f837b60be7eba601443665b41ffde91700d6559757cc21caf4ea4a",
977
+ "language": "Python",
978
+ "lines": 690,
979
+ "truncated": false,
980
+ "block": 3,
981
+ "row": 27377
982
+ },
983
+ {
984
+ "path": "src/scvi/external/gimvi/_module.py",
985
+ "sha256": "706d67027c4dcdd9a7f3c0dc72a5d0115e172065e6b32c18b2211e72c8271a5f",
986
+ "language": "Python",
987
+ "lines": 529,
988
+ "truncated": false,
989
+ "block": 3,
990
+ "row": 26872
991
+ },
992
+ {
993
+ "path": "src/scvi/external/gimvi/_task.py",
994
+ "sha256": "53bcd23ee3415525d8fd6b514fa5c65949f4bccf66b30b2f64d2df5a58d3b333",
995
+ "language": "Python",
996
+ "lines": 195,
997
+ "truncated": false,
998
+ "block": 3,
999
+ "row": 24189
1000
+ },
1001
+ {
1002
+ "path": "src/scvi/external/gimvi/_utils.py",
1003
+ "sha256": "d054b7cf29b198fc66f103cdbb99efba119e5f6587a041ec91a1ba346debb618",
1004
+ "language": "Python",
1005
+ "lines": 125,
1006
+ "truncated": false,
1007
+ "block": 3,
1008
+ "row": 22714
1009
+ },
1010
+ {
1011
+ "path": "src/scvi/external/joint_embedding_scvi/__init__.py",
1012
+ "sha256": "2b4ad58cc24faa78d8a443a76d121963001d47e16f7c9f329236c8ce7b4ab156",
1013
+ "language": "Python",
1014
+ "lines": 4,
1015
+ "truncated": false,
1016
+ "block": 3,
1017
+ "row": 17607
1018
+ },
1019
+ {
1020
+ "path": "src/scvi/external/joint_embedding_scvi/_model.py",
1021
+ "sha256": "9008d6dff7b7dd79d93ffc9e2ae12291c5ea97cebdaa062e87868d814af88572",
1022
+ "language": "Python",
1023
+ "lines": 157,
1024
+ "truncated": false,
1025
+ "block": 3,
1026
+ "row": 23705
1027
+ },
1028
+ {
1029
+ "path": "src/scvi/external/joint_embedding_scvi/_module.py",
1030
+ "sha256": "f86345bc7cf3fbd609c74130ddeeeebe4d499d7da06749f3752da87e0344b135",
1031
+ "language": "Python",
1032
+ "lines": 222,
1033
+ "truncated": false,
1034
+ "block": 3,
1035
+ "row": 24863
1036
+ },
1037
+ {
1038
+ "path": "src/scvi/external/joint_embedding_scvi/_utils.py",
1039
+ "sha256": "b2e0b893134dc2286b478fcd27280a2b63051aa1c8a7a57aeec64166735bc2ae",
1040
+ "language": "Python",
1041
+ "lines": 159,
1042
+ "truncated": false,
1043
+ "block": 3,
1044
+ "row": 23381
1045
+ },
1046
+ {
1047
+ "path": "src/scvi/external/methylvi/__init__.py",
1048
+ "sha256": "0054cff8dcaa794e1dd8f3e1dc07fde884185199d338a3e042d5c4bbc04acac7",
1049
+ "language": "Python",
1050
+ "lines": 17,
1051
+ "truncated": false,
1052
+ "block": 3,
1053
+ "row": 18368
1054
+ },
1055
+ {
1056
+ "path": "src/scvi/external/methylvi/_base_components.py",
1057
+ "sha256": "1668747a0a391c447cddc3321385ee95f3ee6555e3b5ec804cf57b02ebe0d063",
1058
+ "language": "Python",
1059
+ "lines": 525,
1060
+ "truncated": false,
1061
+ "block": 3,
1062
+ "row": 26979
1063
+ },
1064
+ {
1065
+ "path": "src/scvi/external/methylvi/_constants.py",
1066
+ "sha256": "1dc44c6cc7eed068a3d5cee2e9ea51c2f9a45016869bcbcaa2f6758582ca7680",
1067
+ "language": "Python",
1068
+ "lines": 9,
1069
+ "truncated": false,
1070
+ "block": 3,
1071
+ "row": 17672
1072
+ },
1073
+ {
1074
+ "path": "src/scvi/external/methylvi/_methylanvi_model.py",
1075
+ "sha256": "4e5ef1cd73fdb31f31c8afee93fc5a04435be1110025291bf0a7c6e0f8da2318",
1076
+ "language": "Python",
1077
+ "lines": 275,
1078
+ "truncated": false,
1079
+ "block": 3,
1080
+ "row": 24998
1081
+ },
1082
+ {
1083
+ "path": "src/scvi/external/methylvi/_methylanvi_module.py",
1084
+ "sha256": "0b20702620c5438999306b4e706d98e589c59ee3ebecbe56f48150146c63a16d",
1085
+ "language": "Python",
1086
+ "lines": 270,
1087
+ "truncated": false,
1088
+ "block": 3,
1089
+ "row": 25202
1090
+ },
1091
+ {
1092
+ "path": "src/scvi/external/methylvi/_methylvi_model.py",
1093
+ "sha256": "cd610dae62e045d0bb0b9940b3df0d98ad4630da89cd39494fa8a7dbd12a3344",
1094
+ "language": "Python",
1095
+ "lines": 267,
1096
+ "truncated": false,
1097
+ "block": 3,
1098
+ "row": 24692
1099
+ },
1100
+ {
1101
+ "path": "src/scvi/external/methylvi/_methylvi_module.py",
1102
+ "sha256": "e028a52f396b87c4fc5a31034305ae352032a3b289869c8f3351d5c83fb89840",
1103
+ "language": "Python",
1104
+ "lines": 283,
1105
+ "truncated": false,
1106
+ "block": 3,
1107
+ "row": 25130
1108
+ },
1109
+ {
1110
+ "path": "src/scvi/external/methylvi/_utils.py",
1111
+ "sha256": "317ffb22600978a7b5668c1ab45bfb3e88da45144c6f0624379b943aff089933",
1112
+ "language": "Python",
1113
+ "lines": 68,
1114
+ "truncated": false,
1115
+ "block": 3,
1116
+ "row": 20276
1117
+ },
1118
+ {
1119
+ "path": "src/scvi/external/mrvi/__init__.py",
1120
+ "sha256": "52f8960d1504a371f780a081af05dd8a7bf94e73aa54882e983bc5e5bce2cf43",
1121
+ "language": "Python",
1122
+ "lines": 5,
1123
+ "truncated": false,
1124
+ "block": 3,
1125
+ "row": 17549
1126
+ },
1127
+ {
1128
+ "path": "src/scvi/external/mrvi/_components.py",
1129
+ "sha256": "0238b52c8825c714094c1b4ace0b7a12cbd27ba48f1d0080aaf81d65f82f15c2",
1130
+ "language": "Python",
1131
+ "lines": 432,
1132
+ "truncated": false,
1133
+ "block": 3,
1134
+ "row": 26380
1135
+ },
1136
+ {
1137
+ "path": "src/scvi/external/mrvi/_model.py",
1138
+ "sha256": "f954488600016c36095a208f887ae58c3e82625a91b18e5e03161a4123d81568",
1139
+ "language": "Python",
1140
+ "lines": 2083,
1141
+ "truncated": false,
1142
+ "block": 4,
1143
+ "row": 72
1144
+ },
1145
+ {
1146
+ "path": "src/scvi/external/mrvi/_module.py",
1147
+ "sha256": "e503c7e3a70a36ef3605733ff123a7a44a434a7275cf1ecba6f607b082fe4a3b",
1148
+ "language": "Python",
1149
+ "lines": 714,
1150
+ "truncated": false,
1151
+ "block": 3,
1152
+ "row": 27338
1153
+ },
1154
+ {
1155
+ "path": "src/scvi/external/mrvi/_types.py",
1156
+ "sha256": "c7d673574d882d5812c6fe4e5653c5dfc47c416639027bd03b481190684ec5c1",
1157
+ "language": "Python",
1158
+ "lines": 103,
1159
+ "truncated": false,
1160
+ "block": 3,
1161
+ "row": 21597
1162
+ },
1163
+ {
1164
+ "path": "src/scvi/external/mrvi/_utils.py",
1165
+ "sha256": "4f93076c72ed10def3657f2fc37e928f22552af33b55723616dc0b2e4c18de73",
1166
+ "language": "Python",
1167
+ "lines": 25,
1168
+ "truncated": false,
1169
+ "block": 3,
1170
+ "row": 18601
1171
+ },
1172
+ {
1173
+ "path": "src/scvi/external/poissonvi/__init__.py",
1174
+ "sha256": "8da410b1ab68170575952079545e56bc53f36e6f015b9dc2aec3dd14a446868b",
1175
+ "language": "Python",
1176
+ "lines": 3,
1177
+ "truncated": false,
1178
+ "block": 3,
1179
+ "row": 17433
1180
+ },
1181
+ {
1182
+ "path": "src/scvi/external/poissonvi/_model.py",
1183
+ "sha256": "21f6c28f4d0d5ff642a6b18e6ab66d3a2127f6a5993aa7ea2f03683e2d4fe5fb",
1184
+ "language": "Python",
1185
+ "lines": 439,
1186
+ "truncated": false,
1187
+ "block": 3,
1188
+ "row": 26644
1189
+ },
1190
+ {
1191
+ "path": "src/scvi/external/resolvi/__init__.py",
1192
+ "sha256": "d59c39406a780aae74fa80a9fd5d2b272234b0ba10cf63e7034625aa837fecc6",
1193
+ "language": "Python",
1194
+ "lines": 4,
1195
+ "truncated": false,
1196
+ "block": 3,
1197
+ "row": 17512
1198
+ },
1199
+ {
1200
+ "path": "src/scvi/external/resolvi/_model.py",
1201
+ "sha256": "fdf78e7cfef890c3302b99dd52aa95d287f5a807dcb1b39ae886829ec51d9c7b",
1202
+ "language": "Python",
1203
+ "lines": 748,
1204
+ "truncated": false,
1205
+ "block": 3,
1206
+ "row": 27506
1207
+ },
1208
+ {
1209
+ "path": "src/scvi/external/resolvi/_module.py",
1210
+ "sha256": "91aabb8ba7a6aa57a3cea85777c51f29d78db5d6b61ccac6badf1bd0e2a43a44",
1211
+ "language": "Python",
1212
+ "lines": 1329,
1213
+ "truncated": false,
1214
+ "block": 3,
1215
+ "row": 27962
1216
+ },
1217
+ {
1218
+ "path": "src/scvi/external/resolvi/_utils.py",
1219
+ "sha256": "4e82c6e14f4d3127de6b9277e0fbaf612471132f40f744787ee0132c5bd4f05c",
1220
+ "language": "Python",
1221
+ "lines": 566,
1222
+ "truncated": false,
1223
+ "block": 3,
1224
+ "row": 27307
1225
+ },
1226
+ {
1227
+ "path": "src/scvi/external/scar/__init__.py",
1228
+ "sha256": "2a670612feec905d43a019fbe9bc0ac6c341c801d1be127537791f92654941ef",
1229
+ "language": "Python",
1230
+ "lines": 4,
1231
+ "truncated": false,
1232
+ "block": 3,
1233
+ "row": 17496
1234
+ },
1235
+ {
1236
+ "path": "src/scvi/external/scar/_model.py",
1237
+ "sha256": "8bd2adc06c890347e03cf483e48a9fa0ddbbdb46a9bd07f9c8096ac36a7fb781",
1238
+ "language": "Python",
1239
+ "lines": 385,
1240
+ "truncated": false,
1241
+ "block": 3,
1242
+ "row": 26510
1243
+ },
1244
+ {
1245
+ "path": "src/scvi/external/scar/_module.py",
1246
+ "sha256": "fcb52818f7c7bad878d9ccc0f0302ccecb1312356efb0facf724ca34952d7cc5",
1247
+ "language": "Python",
1248
+ "lines": 384,
1249
+ "truncated": false,
1250
+ "block": 3,
1251
+ "row": 26034
1252
+ },
1253
+ {
1254
+ "path": "src/scvi/external/scbasset/__init__.py",
1255
+ "sha256": "5a49691a35f8f748047e09e1c10f5ed73b5a30efafc2ddcf18f93009b5e0139f",
1256
+ "language": "Python",
1257
+ "lines": 4,
1258
+ "truncated": false,
1259
+ "block": 3,
1260
+ "row": 17544
1261
+ },
1262
+ {
1263
+ "path": "src/scvi/external/scbasset/_model.py",
1264
+ "sha256": "1c7ff928e23236984a34c635b1e3a6eee8ed97190a215d6a6236528b3ff5e360",
1265
+ "language": "Python",
1266
+ "lines": 446,
1267
+ "truncated": false,
1268
+ "block": 3,
1269
+ "row": 26788
1270
+ },
1271
+ {
1272
+ "path": "src/scvi/external/scbasset/_module.py",
1273
+ "sha256": "3131d4b1c0aae00ffa1d5c0b15d442bb9ae7562c5e6a6dd207fa8053c1317573",
1274
+ "language": "Python",
1275
+ "lines": 398,
1276
+ "truncated": false,
1277
+ "block": 3,
1278
+ "row": 26269
1279
+ },
1280
+ {
1281
+ "path": "src/scvi/external/scviva/__init__.py",
1282
+ "sha256": "181423f332028516a7816d85838480807fe107e76c115eaec8900e609bf946e5",
1283
+ "language": "Python",
1284
+ "lines": 13,
1285
+ "truncated": false,
1286
+ "block": 3,
1287
+ "row": 17884
1288
+ },
1289
+ {
1290
+ "path": "src/scvi/external/scviva/_components.py",
1291
+ "sha256": "4fb27c02c684addb89cb87a302d8474aca1e2943c1c9c10e93294c3dc839b298",
1292
+ "language": "Python",
1293
+ "lines": 262,
1294
+ "truncated": false,
1295
+ "block": 3,
1296
+ "row": 24365
1297
+ },
1298
+ {
1299
+ "path": "src/scvi/external/scviva/_constants.py",
1300
+ "sha256": "a574f0127293f652027050baa6d2a2f29db3114c567aac5f63c592659d2259ac",
1301
+ "language": "Python",
1302
+ "lines": 30,
1303
+ "truncated": false,
1304
+ "block": 3,
1305
+ "row": 18894
1306
+ },
1307
+ {
1308
+ "path": "src/scvi/external/scviva/_log_likelihood.py",
1309
+ "sha256": "61f5b6e94185312fe576b9ea7121a9ebb15513e17b0cb6a88e567bedd637185f",
1310
+ "language": "Python",
1311
+ "lines": 109,
1312
+ "truncated": false,
1313
+ "block": 3,
1314
+ "row": 22247
1315
+ },
1316
+ {
1317
+ "path": "src/scvi/external/scviva/_model.py",
1318
+ "sha256": "6336a81c42ac88efcff5228822c40facf83bb0d7833978486829e220d052db8b",
1319
+ "language": "Python",
1320
+ "lines": 1173,
1321
+ "truncated": false,
1322
+ "block": 3,
1323
+ "row": 27904
1324
+ },
1325
+ {
1326
+ "path": "src/scvi/external/scviva/_module.py",
1327
+ "sha256": "1ef82f5c4fe3ac1c6841238fc72f959cd3325cd7675896b8043a74e30607cd98",
1328
+ "language": "Python",
1329
+ "lines": 638,
1330
+ "truncated": false,
1331
+ "block": 3,
1332
+ "row": 27410
1333
+ },
1334
+ {
1335
+ "path": "src/scvi/external/scviva/differential_expression/__init__.py",
1336
+ "sha256": "070ef9b33000ad58b8bdd93511b28391ab2882c597f5f4c9da20e90f18148369",
1337
+ "language": "Python",
1338
+ "lines": 11,
1339
+ "truncated": false,
1340
+ "block": 3,
1341
+ "row": 18067
1342
+ },
1343
+ {
1344
+ "path": "src/scvi/external/scviva/differential_expression/_de_utils.py",
1345
+ "sha256": "2fe7311c7e110eec3fd3092ff7accf6f9ce083322ba60322ec615b94b948fc23",
1346
+ "language": "Python",
1347
+ "lines": 113,
1348
+ "truncated": false,
1349
+ "block": 3,
1350
+ "row": 21851
1351
+ },
1352
+ {
1353
+ "path": "src/scvi/external/scviva/differential_expression/_marker_classifier.py",
1354
+ "sha256": "0585f64dfdfe445b48229f233df60bf57e88366fcaf1d4ef8bf400688c7568fb",
1355
+ "language": "Python",
1356
+ "lines": 105,
1357
+ "truncated": false,
1358
+ "block": 3,
1359
+ "row": 21671
1360
+ },
1361
+ {
1362
+ "path": "src/scvi/external/scviva/differential_expression/_niche_de_core.py",
1363
+ "sha256": "c830f176e267c351116bde85b03ddf5d793e397a57bde70c3cf5ff733e086cd8",
1364
+ "language": "Python",
1365
+ "lines": 233,
1366
+ "truncated": false,
1367
+ "block": 3,
1368
+ "row": 24743
1369
+ },
1370
+ {
1371
+ "path": "src/scvi/external/scviva/differential_expression/_results_dataclass.py",
1372
+ "sha256": "5425e623968c59e1ac4007d5c0c9e17d0845cb1e782785f2fde6c3fbb36d29f6",
1373
+ "language": "Python",
1374
+ "lines": 259,
1375
+ "truncated": false,
1376
+ "block": 3,
1377
+ "row": 24986
1378
+ },
1379
+ {
1380
+ "path": "src/scvi/external/solo/__init__.py",
1381
+ "sha256": "1a964b00c6939f34cc3c1e4557f6c535b63d966c57ee99eeafc0a8978dba8e16",
1382
+ "language": "Python",
1383
+ "lines": 3,
1384
+ "truncated": false,
1385
+ "block": 3,
1386
+ "row": 17407
1387
+ },
1388
+ {
1389
+ "path": "src/scvi/external/solo/_model.py",
1390
+ "sha256": "8f8f43c53d1b97aaed828f433c4c1c64d3f709d6395cd07a0e30413b2ff43d8a",
1391
+ "language": "Python",
1392
+ "lines": 484,
1393
+ "truncated": false,
1394
+ "block": 3,
1395
+ "row": 26880
1396
+ },
1397
+ {
1398
+ "path": "src/scvi/external/stereoscope/__init__.py",
1399
+ "sha256": "3fead6e8361efea9bcfbe53422b591b115de298988ea51fdd13ec16d7704698c",
1400
+ "language": "Python",
1401
+ "lines": 4,
1402
+ "truncated": false,
1403
+ "block": 3,
1404
+ "row": 17674
1405
+ },
1406
+ {
1407
+ "path": "src/scvi/external/stereoscope/_model.py",
1408
+ "sha256": "7da1857424e005c0cbf980d7b6f5d020f450f11795fe9714de3c2f7dfb8a514d",
1409
+ "language": "Python",
1410
+ "lines": 394,
1411
+ "truncated": false,
1412
+ "block": 3,
1413
+ "row": 26252
1414
+ },
1415
+ {
1416
+ "path": "src/scvi/external/stereoscope/_module.py",
1417
+ "sha256": "c7ee37d60ee7045d980728867a6d9288e91d58fb6d6cbac49d5bc16ebb2a70ca",
1418
+ "language": "Python",
1419
+ "lines": 265,
1420
+ "truncated": false,
1421
+ "block": 3,
1422
+ "row": 24937
1423
+ },
1424
+ {
1425
+ "path": "src/scvi/external/sysvi/__init__.py",
1426
+ "sha256": "f4af859bbb48279d826dd2012adea82562d17332de6b1f3715e8325131f618ec",
1427
+ "language": "Python",
1428
+ "lines": 4,
1429
+ "truncated": false,
1430
+ "block": 3,
1431
+ "row": 17493
1432
+ },
1433
+ {
1434
+ "path": "src/scvi/external/sysvi/_base_components.py",
1435
+ "sha256": "7649ccc66070d73344ffdb6884f4d7d4e6cf7c1c5330c57c41bbd9de1112578d",
1436
+ "language": "Python",
1437
+ "lines": 221,
1438
+ "truncated": false,
1439
+ "block": 3,
1440
+ "row": 24014
1441
+ },
1442
+ {
1443
+ "path": "src/scvi/external/sysvi/_model.py",
1444
+ "sha256": "cc713254a8decf0ab3663b3dd8ce3629147523877ded758007680c0b0732c372",
1445
+ "language": "Python",
1446
+ "lines": 259,
1447
+ "truncated": false,
1448
+ "block": 3,
1449
+ "row": 25426
1450
+ },
1451
+ {
1452
+ "path": "src/scvi/external/sysvi/_module.py",
1453
+ "sha256": "a3057033ec394aefd424f51fe8b866f6bd868930fe06f10b213a5d846ef7d96e",
1454
+ "language": "Python",
1455
+ "lines": 527,
1456
+ "truncated": false,
1457
+ "block": 3,
1458
+ "row": 26960
1459
+ },
1460
+ {
1461
+ "path": "src/scvi/external/sysvi/_priors.py",
1462
+ "sha256": "68351e7ec135f546e57958e85144c099ebc5cfb233d75cbc213bb6e93dec92a3",
1463
+ "language": "Python",
1464
+ "lines": 206,
1465
+ "truncated": false,
1466
+ "block": 3,
1467
+ "row": 23726
1468
+ },
1469
+ {
1470
+ "path": "src/scvi/external/tangram/__init__.py",
1471
+ "sha256": "203858b21b051d5b22b7e95ed9972e57539f3155998c55188f24b60cc5d3c1a5",
1472
+ "language": "Python",
1473
+ "lines": 4,
1474
+ "truncated": false,
1475
+ "block": 3,
1476
+ "row": 17534
1477
+ },
1478
+ {
1479
+ "path": "src/scvi/external/tangram/_model.py",
1480
+ "sha256": "300b367e827b95ee429dec22a3f3a48b1c4c9a3626043475abb54e6309939f8e",
1481
+ "language": "Python",
1482
+ "lines": 355,
1483
+ "truncated": false,
1484
+ "block": 3,
1485
+ "row": 26086
1486
+ },
1487
+ {
1488
+ "path": "src/scvi/external/tangram/_module.py",
1489
+ "sha256": "b8545a909042efab47135d6811266eb379fe62895a3862745434395573107d8d",
1490
+ "language": "Python",
1491
+ "lines": 164,
1492
+ "truncated": false,
1493
+ "block": 3,
1494
+ "row": 22914
1495
+ },
1496
+ {
1497
+ "path": "src/scvi/external/totalanvi/__init__.py",
1498
+ "sha256": "af6bd52be4264227b879a90e010c1fb3bc5a388ef7c7d922981809d1431ed68f",
1499
+ "language": "Python",
1500
+ "lines": 4,
1501
+ "truncated": false,
1502
+ "block": 3,
1503
+ "row": 17532
1504
+ },
1505
+ {
1506
+ "path": "src/scvi/external/totalanvi/_model.py",
1507
+ "sha256": "ce0158aae127b46ea6216489e25c9c79544c3ae4b8f14038754fcbf2f5e1092d",
1508
+ "language": "Python",
1509
+ "lines": 540,
1510
+ "truncated": false,
1511
+ "block": 3,
1512
+ "row": 27157
1513
+ },
1514
+ {
1515
+ "path": "src/scvi/external/totalanvi/_module.py",
1516
+ "sha256": "b6e2790a4a5e1bbf55b1e56b4258fc9413827fe06ef4f37e04e719c3ef340160",
1517
+ "language": "Python",
1518
+ "lines": 452,
1519
+ "truncated": false,
1520
+ "block": 3,
1521
+ "row": 26796
1522
+ },
1523
+ {
1524
+ "path": "src/scvi/external/velovi/__init__.py",
1525
+ "sha256": "27f5741170e740f95e627e2415a540312a07195b09bf845886d8b4822c254c6f",
1526
+ "language": "Python",
1527
+ "lines": 4,
1528
+ "truncated": false,
1529
+ "block": 3,
1530
+ "row": 17502
1531
+ },
1532
+ {
1533
+ "path": "src/scvi/external/velovi/_constants.py",
1534
+ "sha256": "b9cf40029b23ffcbd542d09837ba828ef2e09cb1445f720465a546245a094b0c",
1535
+ "language": "Python",
1536
+ "lines": 9,
1537
+ "truncated": false,
1538
+ "block": 3,
1539
+ "row": 17636
1540
+ },
1541
+ {
1542
+ "path": "src/scvi/external/velovi/_model.py",
1543
+ "sha256": "9b96766c4e22287b015dba0f4366869c1a0c9aedb8f8dd94f5dcbec94edc2a1a",
1544
+ "language": "Python",
1545
+ "lines": 1153,
1546
+ "truncated": false,
1547
+ "block": 3,
1548
+ "row": 27915
1549
+ },
1550
+ {
1551
+ "path": "src/scvi/external/velovi/_module.py",
1552
+ "sha256": "16d07cbddd88b57568d06c613fac16140ac5bdb76c03f41d88044425fe1cf92c",
1553
+ "language": "Python",
1554
+ "lines": 656,
1555
+ "truncated": false,
1556
+ "block": 3,
1557
+ "row": 27254
1558
+ },
1559
+ {
1560
+ "path": "src/scvi/external/vivs/__init__.py",
1561
+ "sha256": "af0c3b5ac6136b5643e5dd99dd9f26ef2a2fd26ed18defd409ab158889060ad1",
1562
+ "language": "Python",
1563
+ "lines": 15,
1564
+ "truncated": false,
1565
+ "block": 3,
1566
+ "row": 18198
1567
+ },
1568
+ {
1569
+ "path": "src/scvi/external/vivs/_constants.py",
1570
+ "sha256": "f521c3b9bdf62d67c625a1dd8d8ae27682d44987437a3ab65a912fbedd9abc23",
1571
+ "language": "Python",
1572
+ "lines": 10,
1573
+ "truncated": false,
1574
+ "block": 3,
1575
+ "row": 17671
1576
+ },
1577
+ {
1578
+ "path": "src/scvi/external/vivs/_model.py",
1579
+ "sha256": "97618d53fd5dd23d045c9317985baeccbb2c2fae19d771850395a6042d98b9f6",
1580
+ "language": "Python",
1581
+ "lines": 708,
1582
+ "truncated": false,
1583
+ "block": 3,
1584
+ "row": 27565
1585
+ },
1586
+ {
1587
+ "path": "src/scvi/external/vivs/_module.py",
1588
+ "sha256": "745bc82075f7d28d7b3c7b3df461b44330c66393159fa1a58d677ec3bf569f8c",
1589
+ "language": "Python",
1590
+ "lines": 211,
1591
+ "truncated": false,
1592
+ "block": 3,
1593
+ "row": 24920
1594
+ },
1595
+ {
1596
+ "path": "src/scvi/external/vivs/_plotting.py",
1597
+ "sha256": "6266e18dcc5a989fc45b35925543c4e61806908ae58d0d46c1cbf26501233f96",
1598
+ "language": "Python",
1599
+ "lines": 137,
1600
+ "truncated": false,
1601
+ "block": 3,
1602
+ "row": 23076
1603
+ },
1604
+ {
1605
+ "path": "src/scvi/external/vivs/_utils.py",
1606
+ "sha256": "7f2ea482724c4cada6f64864d89541529ca94e89e8410848313ac909fcc5a0b2",
1607
+ "language": "Python",
1608
+ "lines": 94,
1609
+ "truncated": false,
1610
+ "block": 3,
1611
+ "row": 21819
1612
+ },
1613
+ {
1614
+ "path": "src/scvi/hub/__init__.py",
1615
+ "sha256": "f7c29992d076bde540e1fd68a292d6f6ebeeac1dd35372ebf0b83fed2845a39a",
1616
+ "language": "Python",
1617
+ "lines": 8,
1618
+ "truncated": false,
1619
+ "block": 3,
1620
+ "row": 17645
1621
+ },
1622
+ {
1623
+ "path": "src/scvi/hub/_constants.py",
1624
+ "sha256": "5f6676e5df82df83f9f6f8a9219648092d00e3109dc07057421231593d27c06f",
1625
+ "language": "Python",
1626
+ "lines": 26,
1627
+ "truncated": false,
1628
+ "block": 3,
1629
+ "row": 18685
1630
+ },
1631
+ {
1632
+ "path": "src/scvi/hub/_metadata.py",
1633
+ "sha256": "b421e6f5310b9f12248b324715ce3527cfd752b919afe9adcf713fb18d5031fc",
1634
+ "language": "Python",
1635
+ "lines": 364,
1636
+ "truncated": false,
1637
+ "block": 3,
1638
+ "row": 26311
1639
+ },
1640
+ {
1641
+ "path": "src/scvi/hub/_model.py",
1642
+ "sha256": "1d535e87525d049bd140808fc873a81e8f5244f8d088b8e80c063201538a7681",
1643
+ "language": "Python",
1644
+ "lines": 621,
1645
+ "truncated": false,
1646
+ "block": 3,
1647
+ "row": 27343
1648
+ },
1649
+ {
1650
+ "path": "src/scvi/hub/_template.py",
1651
+ "sha256": "aaac06cb41f14d14fca94c4003e2796f7088cb2496cc8e3f3f7f05707d590f92",
1652
+ "language": "Python",
1653
+ "lines": 210,
1654
+ "truncated": false,
1655
+ "block": 3,
1656
+ "row": 24524
1657
+ },
1658
+ {
1659
+ "path": "src/scvi/hub/_url.py",
1660
+ "sha256": "ae6ccd307880f806d484e4bfa48ffb58dd529c3bf251c78704491196f0f4d5ff",
1661
+ "language": "Python",
1662
+ "lines": 57,
1663
+ "truncated": false,
1664
+ "block": 3,
1665
+ "row": 19785
1666
+ },
1667
+ {
1668
+ "path": "src/scvi/model/__init__.py",
1669
+ "sha256": "6c09c225f3e306affaf5afb332f18c05e52360ffd85885440c56c9ce99fbb2cf",
1670
+ "language": "Python",
1671
+ "lines": 51,
1672
+ "truncated": false,
1673
+ "block": 3,
1674
+ "row": 19299
1675
+ },
1676
+ {
1677
+ "path": "src/scvi/model/_amortizedlda.py",
1678
+ "sha256": "9f4423f2afaa3161cf56b475757fc42c126c2373647edf133fa48596fdf4b091",
1679
+ "language": "Python",
1680
+ "lines": 272,
1681
+ "truncated": false,
1682
+ "block": 3,
1683
+ "row": 24974
1684
+ },
1685
+ {
1686
+ "path": "src/scvi/model/_autozi.py",
1687
+ "sha256": "ee550ab2915f3bb8c27e95405ba8b39539774f2f6d4c2278ded08173ae95bd2f",
1688
+ "language": "Python",
1689
+ "lines": 295,
1690
+ "truncated": false,
1691
+ "block": 3,
1692
+ "row": 25725
1693
+ },
1694
+ {
1695
+ "path": "src/scvi/model/_condscvi.py",
1696
+ "sha256": "54da234838e8b2cf73809bf37e06029f4c40eadccdae21ab1415a03063be4e07",
1697
+ "language": "Python",
1698
+ "lines": 471,
1699
+ "truncated": false,
1700
+ "block": 3,
1701
+ "row": 26777
1702
+ },
1703
+ {
1704
+ "path": "src/scvi/model/_destvi.py",
1705
+ "sha256": "249f16b97ec99fd824ba5c870c59c7666abc59bf49221817a7684adaf198c5e4",
1706
+ "language": "Python",
1707
+ "lines": 700,
1708
+ "truncated": false,
1709
+ "block": 3,
1710
+ "row": 27492
1711
+ },
1712
+ {
1713
+ "path": "src/scvi/model/_linear_scvi.py",
1714
+ "sha256": "71cb3b2260bb7518b949e6359de83b6c6c1173aff31bd87d18e1fdb002eda4c8",
1715
+ "language": "Python",
1716
+ "lines": 192,
1717
+ "truncated": false,
1718
+ "block": 3,
1719
+ "row": 23845
1720
+ },
1721
+ {
1722
+ "path": "src/scvi/model/_mlxscvi.py",
1723
+ "sha256": "2e87fc5ae6df986e92a390476be6cd52a1f89ff95ddd3d26c0ae6fea8f2568df",
1724
+ "language": "Python",
1725
+ "lines": 216,
1726
+ "truncated": false,
1727
+ "block": 3,
1728
+ "row": 23972
1729
+ },
1730
+ {
1731
+ "path": "src/scvi/model/_multivi.py",
1732
+ "sha256": "9d43a0dd3a832d6d92166741051cbc64bf0bce3bbd3f68eb43fb7d0478acb8c8",
1733
+ "language": "Python",
1734
+ "lines": 1282,
1735
+ "truncated": false,
1736
+ "block": 3,
1737
+ "row": 27968
1738
+ },
1739
+ {
1740
+ "path": "src/scvi/model/_peakvi.py",
1741
+ "sha256": "4fd3c7ab4bc0ffd32fb928c37d3451ba69882c1518ee23aa688ba782bd3b6386",
1742
+ "language": "Python",
1743
+ "lines": 665,
1744
+ "truncated": false,
1745
+ "block": 3,
1746
+ "row": 27415
1747
+ },
1748
+ {
1749
+ "path": "src/scvi/model/_scanvi.py",
1750
+ "sha256": "5671c148923c4fe5f3789ca6d31c8ddd36f416311180130b768f00e283781a7e",
1751
+ "language": "Python",
1752
+ "lines": 345,
1753
+ "truncated": false,
1754
+ "block": 3,
1755
+ "row": 26109
1756
+ },
1757
+ {
1758
+ "path": "src/scvi/model/_scvi.py",
1759
+ "sha256": "b9c27545170b15989dafdb16a63879ebd37d1ab9107520b5987357a8362619b8",
1760
+ "language": "Python",
1761
+ "lines": 258,
1762
+ "truncated": false,
1763
+ "block": 3,
1764
+ "row": 25184
1765
+ },
1766
+ {
1767
+ "path": "src/scvi/model/_totalvi.py",
1768
+ "sha256": "a2476eddb84d5b52d463d82caa00acce5ade8cd82335e17a2c24fc8b78433665",
1769
+ "language": "Python",
1770
+ "lines": 1557,
1771
+ "truncated": false,
1772
+ "block": 3,
1773
+ "row": 28040
1774
+ },
1775
+ {
1776
+ "path": "src/scvi/model/_utils.py",
1777
+ "sha256": "46aa97aa931827c2b0422e45d7ea338962589120fc96e2beabc393614ccc5e24",
1778
+ "language": "Python",
1779
+ "lines": 427,
1780
+ "truncated": false,
1781
+ "block": 3,
1782
+ "row": 26620
1783
+ },
1784
+ {
1785
+ "path": "src/scvi/model/base/__init__.py",
1786
+ "sha256": "710c3c8a7c8500a5ae0c6b48ae7200be3a891c710ca51fff28f9c70753d41bbc",
1787
+ "language": "Python",
1788
+ "lines": 58,
1789
+ "truncated": false,
1790
+ "block": 3,
1791
+ "row": 19729
1792
+ },
1793
+ {
1794
+ "path": "src/scvi/model/base/_archesmixin.py",
1795
+ "sha256": "8aef1ecf82c2b7ab9891bc5bae449ac5e04f88da40fc09ae7abdf3483315e6ed",
1796
+ "language": "Python",
1797
+ "lines": 540,
1798
+ "truncated": false,
1799
+ "block": 3,
1800
+ "row": 27161
1801
+ },
1802
+ {
1803
+ "path": "src/scvi/model/base/_base_model.py",
1804
+ "sha256": "9da3a14751926100fc40608b265c0dbb694a3bd86186ab51c40a147a575ca53b",
1805
+ "language": "Python",
1806
+ "lines": 2016,
1807
+ "truncated": false,
1808
+ "block": 4,
1809
+ "row": 66
1810
+ },
1811
+ {
1812
+ "path": "src/scvi/model/base/_constants.py",
1813
+ "sha256": "a574719de17c376e2af8926c388d373dd2d14ee93cd9bc9301e902fc38bbb5b9",
1814
+ "language": "Python",
1815
+ "lines": 16,
1816
+ "truncated": false,
1817
+ "block": 3,
1818
+ "row": 18326
1819
+ },
1820
+ {
1821
+ "path": "src/scvi/model/base/_de_core.py",
1822
+ "sha256": "5cd7e3763ac4aba405d59ac7e8c635776d2342b1ca1c43958bc47abb5aed6da6",
1823
+ "language": "Python",
1824
+ "lines": 219,
1825
+ "truncated": false,
1826
+ "block": 3,
1827
+ "row": 24009
1828
+ },
1829
+ {
1830
+ "path": "src/scvi/model/base/_differential.py",
1831
+ "sha256": "ff7ea46fe16af3f8b5a26369807c6fa549741cdccd10bec45451af0d268e3cec",
1832
+ "language": "Python",
1833
+ "lines": 743,
1834
+ "truncated": false,
1835
+ "block": 3,
1836
+ "row": 27535
1837
+ },
1838
+ {
1839
+ "path": "src/scvi/model/base/_embedding_mixin.py",
1840
+ "sha256": "26ba882984495f6745a7a825b058ee7a97c3e4db58da4b619f934b1022bf4bd9",
1841
+ "language": "Python",
1842
+ "lines": 38,
1843
+ "truncated": false,
1844
+ "block": 3,
1845
+ "row": 19238
1846
+ },
1847
+ {
1848
+ "path": "src/scvi/model/base/_log_likelihood.py",
1849
+ "sha256": "f548c55936c08b6eb2c9a9d2d4bdcf65ea8d9c453ce5c2e6b0b314597b95e2af",
1850
+ "language": "Python",
1851
+ "lines": 136,
1852
+ "truncated": false,
1853
+ "block": 3,
1854
+ "row": 23147
1855
+ },
1856
+ {
1857
+ "path": "src/scvi/model/base/_mlxmixin.py",
1858
+ "sha256": "285079398212c0be2d3ffd7ee57d799a023baf336134311980f7c1e417d1544e",
1859
+ "language": "Python",
1860
+ "lines": 283,
1861
+ "truncated": false,
1862
+ "block": 3,
1863
+ "row": 25483
1864
+ },
1865
+ {
1866
+ "path": "src/scvi/model/base/_pyromixin.py",
1867
+ "sha256": "55127510a1f55217c0021c844d0574416e506d473a2727a9faeb9671cacd179b",
1868
+ "language": "Python",
1869
+ "lines": 718,
1870
+ "truncated": false,
1871
+ "block": 3,
1872
+ "row": 27498
1873
+ },
1874
+ {
1875
+ "path": "src/scvi/model/base/_rnamixin.py",
1876
+ "sha256": "2068228abd8ba1839c28e042ab556d53dbf5f91b75119e748fb7280202a4c010",
1877
+ "language": "Python",
1878
+ "lines": 963,
1879
+ "truncated": false,
1880
+ "block": 3,
1881
+ "row": 27799
1882
+ },
1883
+ {
1884
+ "path": "src/scvi/model/base/_save_load.py",
1885
+ "sha256": "8fecd815bb579644f645f4027d4b41e86fbcac6d075dba333670d75c30d6ac25",
1886
+ "language": "Python",
1887
+ "lines": 246,
1888
+ "truncated": false,
1889
+ "block": 3,
1890
+ "row": 24928
1891
+ },
1892
+ {
1893
+ "path": "src/scvi/model/base/_training_mixin.py",
1894
+ "sha256": "706bf9dda461c1cf581d2e4444d2bce251771dae4f96753312e03e0c7c78fd19",
1895
+ "language": "Python",
1896
+ "lines": 714,
1897
+ "truncated": false,
1898
+ "block": 3,
1899
+ "row": 27569
1900
+ },
1901
+ {
1902
+ "path": "src/scvi/model/base/_vaemixin.py",
1903
+ "sha256": "85c1eab60776887a812c4de23fb5d7d2924eceabf58923a96c490622a42334c5",
1904
+ "language": "Python",
1905
+ "lines": 540,
1906
+ "truncated": false,
1907
+ "block": 3,
1908
+ "row": 27239
1909
+ },
1910
+ {
1911
+ "path": "src/scvi/model/utils/__init__.py",
1912
+ "sha256": "90e8f863fbb6ffcf857a9fa48ebfb98b69b20231d82563a13d8fec042d168e64",
1913
+ "language": "Python",
1914
+ "lines": 17,
1915
+ "truncated": false,
1916
+ "block": 3,
1917
+ "row": 18460
1918
+ },
1919
+ {
1920
+ "path": "src/scvi/model/utils/_annbatch_de_core.py",
1921
+ "sha256": "ac4b9c13ef76c92fa024f9efd0c077745e4c6dc855560bc2654bea9b42e24a25",
1922
+ "language": "Python",
1923
+ "lines": 471,
1924
+ "truncated": false,
1925
+ "block": 3,
1926
+ "row": 26525
1927
+ },
1928
+ {
1929
+ "path": "src/scvi/model/utils/_minification.py",
1930
+ "sha256": "3bfbd19387dd9439670865aad4648daa2dd136b6602a6b1082a489ca4b729868",
1931
+ "language": "Python",
1932
+ "lines": 67,
1933
+ "truncated": false,
1934
+ "block": 3,
1935
+ "row": 20180
1936
+ },
1937
+ {
1938
+ "path": "src/scvi/module/__init__.py",
1939
+ "sha256": "3a210cb6926aa551f9744356cf4fea465c66a859a2f0f6dc32b13d411e1bc948",
1940
+ "language": "Python",
1941
+ "lines": 48,
1942
+ "truncated": false,
1943
+ "block": 3,
1944
+ "row": 19202
1945
+ },
1946
+ {
1947
+ "path": "src/scvi/module/_amortizedlda.py",
1948
+ "sha256": "49ae347e9051a87b44b2011ee141e6f88015b25465423ac57baa7116c197877f",
1949
+ "language": "Python",
1950
+ "lines": 361,
1951
+ "truncated": false,
1952
+ "block": 3,
1953
+ "row": 25969
1954
+ },
1955
+ {
1956
+ "path": "src/scvi/module/_autozivae.py",
1957
+ "sha256": "3869e9d5f7284735dcd53cb2b48e0d630b7ec7bf1b5396be595fd51232af5529",
1958
+ "language": "Python",
1959
+ "lines": 413,
1960
+ "truncated": false,
1961
+ "block": 3,
1962
+ "row": 26691
1963
+ },
1964
+ {
1965
+ "path": "src/scvi/module/_classifier.py",
1966
+ "sha256": "971c87f42ade25b0da9b6a9f1d6b5e33503c5845c66f711886ccf38b619c2a52",
1967
+ "language": "Python",
1968
+ "lines": 79,
1969
+ "truncated": false,
1970
+ "block": 3,
1971
+ "row": 20394
1972
+ },
1973
+ {
1974
+ "path": "src/scvi/module/_constants.py",
1975
+ "sha256": "70a3f7ecec6db4a8cedaa3b835d1309bbc4ab36a90186c6f26a293291c08b5ab",
1976
+ "language": "Python",
1977
+ "lines": 27,
1978
+ "truncated": false,
1979
+ "block": 3,
1980
+ "row": 18527
1981
+ },
1982
+ {
1983
+ "path": "src/scvi/module/_mlxvae.py",
1984
+ "sha256": "b5981d061cf63a434d121fb0a0ae83232645b86046fdc3a47e9d7ab5f9f49949",
1985
+ "language": "Python",
1986
+ "lines": 392,
1987
+ "truncated": false,
1988
+ "block": 3,
1989
+ "row": 26249
1990
+ },
1991
+ {
1992
+ "path": "src/scvi/module/_mrdeconv.py",
1993
+ "sha256": "f289d4837ef4afed461cf9a7a4934149c51552d84f2840659551b1a448abfe0d",
1994
+ "language": "Python",
1995
+ "lines": 676,
1996
+ "truncated": false,
1997
+ "block": 3,
1998
+ "row": 27502
1999
+ },
2000
+ {
2001
+ "path": "src/scvi/module/_multivae.py",
2002
+ "sha256": "eb3cd269062b30555bf6b0b0a2b73a0808f958168b03f162e4fbdcdf6baa53b0",
2003
+ "language": "Python",
2004
+ "lines": 1060,
2005
+ "truncated": false,
2006
+ "block": 3,
2007
+ "row": 27861
2008
+ },
2009
+ {
2010
+ "path": "src/scvi/module/_peakvae.py",
2011
+ "sha256": "e07cee86940b5b096e7371a7a65b3a46eed61c66f67d2a41a8fafd10d72dd5d8",
2012
+ "language": "Python",
2013
+ "lines": 348,
2014
+ "truncated": false,
2015
+ "block": 3,
2016
+ "row": 26038
2017
+ },
2018
+ {
2019
+ "path": "src/scvi/module/_scanvae.py",
2020
+ "sha256": "ffc3ff49c7b3d885e4a5708208845f1a2e4420c1865be63043f6b97e1b6992ef",
2021
+ "language": "Python",
2022
+ "lines": 278,
2023
+ "truncated": false,
2024
+ "block": 3,
2025
+ "row": 25377
2026
+ },
2027
+ {
2028
+ "path": "src/scvi/module/_totalvae.py",
2029
+ "sha256": "6ec762c88f5e40a236340bd54186d01ff13f248ac8af13284456550de14e35f5",
2030
+ "language": "Python",
2031
+ "lines": 866,
2032
+ "truncated": false,
2033
+ "block": 3,
2034
+ "row": 27749
2035
+ },
2036
+ {
2037
+ "path": "src/scvi/module/_utils.py",
2038
+ "sha256": "bbfab4535afd72e18482c2379989fcb8ee0f59f153b91e21d9e13c433fef7f19",
2039
+ "language": "Python",
2040
+ "lines": 32,
2041
+ "truncated": false,
2042
+ "block": 3,
2043
+ "row": 19253
2044
+ },
2045
+ {
2046
+ "path": "src/scvi/module/_vae.py",
2047
+ "sha256": "fdff88c882872df625c3563aaa3fa0333ff33f244accb8629fa6d30c3f575d1c",
2048
+ "language": "Python",
2049
+ "lines": 893,
2050
+ "truncated": false,
2051
+ "block": 3,
2052
+ "row": 27743
2053
+ },
2054
+ {
2055
+ "path": "src/scvi/module/_vaec.py",
2056
+ "sha256": "0e8db2da342ed7e9d3835c15407a0f734c87d704a0c083cabeef5a4398456598",
2057
+ "language": "Python",
2058
+ "lines": 382,
2059
+ "truncated": false,
2060
+ "block": 3,
2061
+ "row": 26248
2062
+ },
2063
+ {
2064
+ "path": "src/scvi/module/base/__init__.py",
2065
+ "sha256": "853cdd5c98d67b17f471cc350ed35876f3be39605315fef80d9bdde252493dc7",
2066
+ "language": "Python",
2067
+ "lines": 25,
2068
+ "truncated": false,
2069
+ "block": 3,
2070
+ "row": 18493
2071
+ },
2072
+ {
2073
+ "path": "src/scvi/module/base/_base_module.py",
2074
+ "sha256": "04a8cde603cbf9408fd4cffcfa0c39407591cd405db481cf880b3567f01efb60",
2075
+ "language": "Python",
2076
+ "lines": 595,
2077
+ "truncated": false,
2078
+ "block": 3,
2079
+ "row": 27233
2080
+ },
2081
+ {
2082
+ "path": "src/scvi/module/base/_decorators.py",
2083
+ "sha256": "afae092fe90ce03b710a8ffd07777d73d2dbe52a4a963f89fbc597f8734d0d08",
2084
+ "language": "Python",
2085
+ "lines": 116,
2086
+ "truncated": false,
2087
+ "block": 3,
2088
+ "row": 21827
2089
+ },
2090
+ {
2091
+ "path": "src/scvi/module/base/_embedding_mixin.py",
2092
+ "sha256": "f1951715722aaf417f6e212f14f6208790b916e6529deec191f7c31da4d5a8d2",
2093
+ "language": "Python",
2094
+ "lines": 50,
2095
+ "truncated": false,
2096
+ "block": 3,
2097
+ "row": 19960
2098
+ },
2099
+ {
2100
+ "path": "src/scvi/module/base/_priors.py",
2101
+ "sha256": "0a15731dbc9b72b40bfdca935d9c58d32a72e6ddb7c0850f14bf27df61d61cfa",
2102
+ "language": "Python",
2103
+ "lines": 301,
2104
+ "truncated": false,
2105
+ "block": 3,
2106
+ "row": 25304
2107
+ },
2108
+ {
2109
+ "path": "src/scvi/module/base/_pyro.py",
2110
+ "sha256": "5a22b99c8b6e3ea1db9bdf6318733db3a6152214b1e5c2ee9fe55197d2ab373a",
2111
+ "language": "Python",
2112
+ "lines": 11,
2113
+ "truncated": false,
2114
+ "block": 3,
2115
+ "row": 17793
2116
+ },
2117
+ {
2118
+ "path": "src/scvi/nn/__init__.py",
2119
+ "sha256": "0bc20176f7fa6e94e85ed597e48d0e38892ae0dd52793a947b838517411a06ca",
2120
+ "language": "Python",
2121
+ "lines": 28,
2122
+ "truncated": false,
2123
+ "block": 3,
2124
+ "row": 18354
2125
+ },
2126
+ {
2127
+ "path": "src/scvi/nn/_base_components.py",
2128
+ "sha256": "8a36fffdd30c7b46c7b98a901061aeb3062305ab91cbb6dcf8739d91066c4469",
2129
+ "language": "Python",
2130
+ "lines": 1099,
2131
+ "truncated": false,
2132
+ "block": 3,
2133
+ "row": 27780
2134
+ },
2135
+ {
2136
+ "path": "src/scvi/nn/_embedding.py",
2137
+ "sha256": "65b4a753726bfaf599ca9e389905d50cfca46609ba3493200c7a020fed47e96f",
2138
+ "language": "Python",
2139
+ "lines": 98,
2140
+ "truncated": false,
2141
+ "block": 3,
2142
+ "row": 21955
2143
+ },
2144
+ {
2145
+ "path": "src/scvi/nn/_utils.py",
2146
+ "sha256": "f2714081abc7e9fa46f22d289f5c21398f540a7d686c5bf5dd672c3a8bce48e4",
2147
+ "language": "Python",
2148
+ "lines": 10,
2149
+ "truncated": false,
2150
+ "block": 3,
2151
+ "row": 17673
2152
+ },
2153
+ {
2154
+ "path": "src/scvi/train/__init__.py",
2155
+ "sha256": "999064308beb34599e95cc63ef54efe7511e14c95a4a4450e0b3b41ac115a907",
2156
+ "language": "Python",
2157
+ "lines": 70,
2158
+ "truncated": false,
2159
+ "block": 3,
2160
+ "row": 20054
2161
+ },
2162
+ {
2163
+ "path": "src/scvi/train/_callbacks.py",
2164
+ "sha256": "6d08dde879db4bf6699e4dd893f273c432a459c7eca5c736402b49a9539347ed",
2165
+ "language": "Python",
2166
+ "lines": 285,
2167
+ "truncated": false,
2168
+ "block": 3,
2169
+ "row": 25737
2170
+ },
2171
+ {
2172
+ "path": "src/scvi/train/_config.py",
2173
+ "sha256": "f019d9cff5f87e551394e202456b34518eaeba1ac9d59cd003efc608da9c5a0b",
2174
+ "language": "Python",
2175
+ "lines": 388,
2176
+ "truncated": false,
2177
+ "block": 3,
2178
+ "row": 26275
2179
+ },
2180
+ {
2181
+ "path": "src/scvi/train/_constants.py",
2182
+ "sha256": "b3adfe17644837bdf9217cbadb66ebc12b0b784ebcd529c2f84f612839669cd9",
2183
+ "language": "Python",
2184
+ "lines": 17,
2185
+ "truncated": false,
2186
+ "block": 3,
2187
+ "row": 18341
2188
+ },
2189
+ {
2190
+ "path": "src/scvi/train/_logger.py",
2191
+ "sha256": "e06baf5c14a2984cee6fa6076cd71e92b0755ca0fee5767780afd3b46495bf4f",
2192
+ "language": "Python",
2193
+ "lines": 124,
2194
+ "truncated": false,
2195
+ "block": 3,
2196
+ "row": 22088
2197
+ },
2198
+ {
2199
+ "path": "src/scvi/train/_metrics.py",
2200
+ "sha256": "beaf6caf5bf5bb63817a54f87cc4e1d247b1f913d0264a859c0ad11d5d3117cf",
2201
+ "language": "Python",
2202
+ "lines": 91,
2203
+ "truncated": false,
2204
+ "block": 3,
2205
+ "row": 21003
2206
+ },
2207
+ {
2208
+ "path": "src/scvi/train/_progress.py",
2209
+ "sha256": "5091b9afcf397a3d1679672bc902fb1cae32c5a10c898bad5c35f0d42fe08f9a",
2210
+ "language": "Python",
2211
+ "lines": 91,
2212
+ "truncated": false,
2213
+ "block": 3,
2214
+ "row": 21206
2215
+ },
2216
+ {
2217
+ "path": "src/scvi/train/_trainer.py",
2218
+ "sha256": "74b67e1e837a7bdb080ee8a0c9af5a430df6b00130bb1475847a825d0147776f",
2219
+ "language": "Python",
2220
+ "lines": 228,
2221
+ "truncated": false,
2222
+ "block": 3,
2223
+ "row": 25394
2224
+ },
2225
+ {
2226
+ "path": "src/scvi/train/_trainingplans.py",
2227
+ "sha256": "d2e6f646dff0cf0aae192bcd0f351c3903266e48ead0cfe4e4c65e055937a0b3",
2228
+ "language": "Python",
2229
+ "lines": 1927,
2230
+ "truncated": false,
2231
+ "block": 4,
2232
+ "row": 51
2233
+ },
2234
+ {
2235
+ "path": "src/scvi/train/_trainrunner.py",
2236
+ "sha256": "e56357d0e796efdac40e66599e36ab2aa5dfeefbd6bce080de265c0c77cd465d",
2237
+ "language": "Python",
2238
+ "lines": 269,
2239
+ "truncated": false,
2240
+ "block": 3,
2241
+ "row": 25524
2242
+ },
2243
+ {
2244
+ "path": "src/scvi/utils/__init__.py",
2245
+ "sha256": "4eca160be556da2639ba9b6abd83208dddc6052cf23b4549e7eb6bf2a000c639",
2246
+ "language": "Python",
2247
+ "lines": 21,
2248
+ "truncated": false,
2249
+ "block": 3,
2250
+ "row": 18551
2251
+ },
2252
+ {
2253
+ "path": "src/scvi/utils/_attrdict.py",
2254
+ "sha256": "887deda162f6033e94a68620bc0120fb81f7ac1dd72c9088223fe9d9adefc336",
2255
+ "language": "Python",
2256
+ "lines": 12,
2257
+ "truncated": false,
2258
+ "block": 3,
2259
+ "row": 18223
2260
+ },
2261
+ {
2262
+ "path": "src/scvi/utils/_decorators.py",
2263
+ "sha256": "7382fda0e0584e7277401f6852498cc88f5f624b72b3255b57082cb5f153c0a9",
2264
+ "language": "Python",
2265
+ "lines": 18,
2266
+ "truncated": false,
2267
+ "block": 3,
2268
+ "row": 18488
2269
+ },
2270
+ {
2271
+ "path": "src/scvi/utils/_dependencies.py",
2272
+ "sha256": "d62e4f1cd74c57a55887ba450f306429e9602562819b2538a9d68a45fd97ba2d",
2273
+ "language": "Python",
2274
+ "lines": 44,
2275
+ "truncated": false,
2276
+ "block": 3,
2277
+ "row": 19390
2278
+ },
2279
+ {
2280
+ "path": "src/scvi/utils/_docstrings.py",
2281
+ "sha256": "e7fda2a0d21a4e19b8b8db212dac45e562e8915b0e894cbf4d78e7aecced8c74",
2282
+ "language": "Python",
2283
+ "lines": 258,
2284
+ "truncated": false,
2285
+ "block": 3,
2286
+ "row": 25193
2287
+ },
2288
+ {
2289
+ "path": "src/scvi/utils/_mlflow.py",
2290
+ "sha256": "b7c2ee4a7d6cc3af891ab4e6aa79374eb1aef51ed05da46ce11400476cdbfa50",
2291
+ "language": "Python",
2292
+ "lines": 144,
2293
+ "truncated": false,
2294
+ "block": 3,
2295
+ "row": 23295
2296
+ },
2297
+ {
2298
+ "path": "src/scvi/utils/_track.py",
2299
+ "sha256": "69b3004b822c8e3837949dc70a3a2a17d049c1f65c08d48306e1abf42362c99c",
2300
+ "language": "Python",
2301
+ "lines": 59,
2302
+ "truncated": false,
2303
+ "block": 3,
2304
+ "row": 19884
2305
+ },
2306
+ {
2307
+ "path": "tests/autotune/test_experiment.py",
2308
+ "sha256": "81fb82cf8a5f01f649dc98211f8019a65078d8de9b843806cc07ec11c982df76",
2309
+ "language": "Python",
2310
+ "lines": 1181,
2311
+ "truncated": false,
2312
+ "block": 3,
2313
+ "row": 27640
2314
+ },
2315
+ {
2316
+ "path": "tests/autotune/test_tune.py",
2317
+ "sha256": "91e436ed18f32a47ab7dcde0b32ff7f6b61b932cef036862e85dfd5c03ee7972",
2318
+ "language": "Python",
2319
+ "lines": 336,
2320
+ "truncated": false,
2321
+ "block": 3,
2322
+ "row": 25214
2323
+ },
2324
+ {
2325
+ "path": "tests/conftest.py",
2326
+ "sha256": "668e9a999081691ec48607ffd08fce47f7c2a7a425ae127451c910b3147e97a8",
2327
+ "language": "Python",
2328
+ "lines": 168,
2329
+ "truncated": false,
2330
+ "block": 3,
2331
+ "row": 24170
2332
+ },
2333
+ {
2334
+ "path": "tests/criticism/test_criticism.py",
2335
+ "sha256": "f1a75a36bc68baaee72739e1cd71388f3d23aa24975d170cd2cb1b9e18bd9182",
2336
+ "language": "Python",
2337
+ "lines": 122,
2338
+ "truncated": false,
2339
+ "block": 3,
2340
+ "row": 22149
2341
+ },
2342
+ {
2343
+ "path": "tests/data/conftest.py",
2344
+ "sha256": "742adb339d12f822e8a9f5c7a9754045d811d6ca697ef72123c8997fd2b65950",
2345
+ "language": "Python",
2346
+ "lines": 20,
2347
+ "truncated": false,
2348
+ "block": 3,
2349
+ "row": 18424
2350
+ },
2351
+ {
2352
+ "path": "tests/data/test_anndata.py",
2353
+ "sha256": "1f6785f1f5988f4e20fd03f3ac644dff21da163044877916497920fb498d37de",
2354
+ "language": "Python",
2355
+ "lines": 548,
2356
+ "truncated": false,
2357
+ "block": 3,
2358
+ "row": 27087
2359
+ },
2360
+ {
2361
+ "path": "tests/data/test_anntorchdataset.py",
2362
+ "sha256": "e953ef04d9945a6fa34810e9b4d5deb2103cec518d4c9a5cfe3416f06a4d5e6c",
2363
+ "language": "Python",
2364
+ "lines": 176,
2365
+ "truncated": false,
2366
+ "block": 3,
2367
+ "row": 24152
2368
+ },
2369
+ {
2370
+ "path": "tests/data/test_built_in_data.py",
2371
+ "sha256": "695c0667f6a723ebad9236ae3c282c3cf1c1496892c93ccd35ef28d2269c0261",
2372
+ "language": "Python",
2373
+ "lines": 112,
2374
+ "truncated": false,
2375
+ "block": 3,
2376
+ "row": 21402
2377
+ },
2378
+ {
2379
+ "path": "tests/data/test_data_utils.py",
2380
+ "sha256": "8b4640288055e20e0fadd5f1bdbb4c55ffbcfcb75aaf31c70db20d7829234d84",
2381
+ "language": "Python",
2382
+ "lines": 32,
2383
+ "truncated": false,
2384
+ "block": 3,
2385
+ "row": 18982
2386
+ },
2387
+ {
2388
+ "path": "tests/data/test_dataset10X.py",
2389
+ "sha256": "9230f2e20a50eaa087b588aef8576017d4ffe7b2c720d390775ec05b64d5ba14",
2390
+ "language": "Python",
2391
+ "lines": 47,
2392
+ "truncated": false,
2393
+ "block": 3,
2394
+ "row": 19297
2395
+ },
2396
+ {
2397
+ "path": "tests/data/test_mudata.py",
2398
+ "sha256": "4df4dc1ecc96eaa928b2489363e9e54b457d67a6b20dbd3a256a98487388966d",
2399
+ "language": "Python",
2400
+ "lines": 394,
2401
+ "truncated": false,
2402
+ "block": 3,
2403
+ "row": 26310
2404
+ },
2405
+ {
2406
+ "path": "tests/data/test_preprocessing.py",
2407
+ "sha256": "fe6a92ef64799b3eebcc5765296d17f4c96462d9d4a105c327a2ccf5954f899a",
2408
+ "language": "Python",
2409
+ "lines": 104,
2410
+ "truncated": false,
2411
+ "block": 3,
2412
+ "row": 21546
2413
+ },
2414
+ {
2415
+ "path": "tests/data/test_synthetic_iid.py",
2416
+ "sha256": "f6ba9faa42e5ecf1c86e06ee5769915fbf6efe200444efa991e5874f4f958299",
2417
+ "language": "Python",
2418
+ "lines": 17,
2419
+ "truncated": false,
2420
+ "block": 3,
2421
+ "row": 18518
2422
+ },
2423
+ {
2424
+ "path": "tests/data/utils.py",
2425
+ "sha256": "45b295c67be486df96321f93e7a65ee447ebb7681b7ce231e112bbeb69885606",
2426
+ "language": "Python",
2427
+ "lines": 142,
2428
+ "truncated": false,
2429
+ "block": 3,
2430
+ "row": 22879
2431
+ },
2432
+ {
2433
+ "path": "tests/dataloaders/sparse_utils.py",
2434
+ "sha256": "0d6173af5e515e259d50487fbd80ed110043dd62136a9943e19ce451a577cd1c",
2435
+ "language": "Python",
2436
+ "lines": 118,
2437
+ "truncated": false,
2438
+ "block": 3,
2439
+ "row": 21799
2440
+ },
2441
+ {
2442
+ "path": "tests/dataloaders/test_annbatch.py",
2443
+ "sha256": "8bbb475e77059f8123d1049bf8752c31fd9d3e415c69aa7938fd667187604a20",
2444
+ "language": "Python",
2445
+ "lines": 1014,
2446
+ "truncated": false,
2447
+ "block": 3,
2448
+ "row": 27715
2449
+ },
2450
+ {
2451
+ "path": "tests/dataloaders/test_custom_dataloader.py",
2452
+ "sha256": "42cc2a3d915cdffb2c3deb060fee87ee22712e6621cc3fcee10c6b1c36279be5",
2453
+ "language": "Python",
2454
+ "lines": 1205,
2455
+ "truncated": false,
2456
+ "block": 3,
2457
+ "row": 27929
2458
+ },
2459
+ {
2460
+ "path": "tests/dataloaders/test_dataloaders.py",
2461
+ "sha256": "3bff9d5e8324ef199453e92cbb4be29f0056519a7b81fa0c537c58522d64ed1b",
2462
+ "language": "Python",
2463
+ "lines": 301,
2464
+ "truncated": false,
2465
+ "block": 3,
2466
+ "row": 25171
2467
+ },
2468
+ {
2469
+ "path": "tests/dataloaders/test_datasplitter.py",
2470
+ "sha256": "be53a6c6b2cc4d4099caec706cb778453baee97fbcecb96f6dd86f58e4f3c2b6",
2471
+ "language": "Python",
2472
+ "lines": 272,
2473
+ "truncated": false,
2474
+ "block": 3,
2475
+ "row": 25728
2476
+ },
2477
+ {
2478
+ "path": "tests/dataloaders/test_samplers.py",
2479
+ "sha256": "9a04f149cad31e76351c65fa5de2bc29d79796aba99a39cc9d5ae77dfa7b26e4",
2480
+ "language": "Python",
2481
+ "lines": 155,
2482
+ "truncated": false,
2483
+ "block": 3,
2484
+ "row": 23167
2485
+ },
2486
+ {
2487
+ "path": "tests/distributions/test_beta_binomial.py",
2488
+ "sha256": "0769cf5802d4a84e12c9c740184c0086ae0a3291f9ac780be29d078d1dba08f6",
2489
+ "language": "Python",
2490
+ "lines": 77,
2491
+ "truncated": false,
2492
+ "block": 3,
2493
+ "row": 20883
2494
+ },
2495
+ {
2496
+ "path": "tests/distributions/test_constraints.py",
2497
+ "sha256": "d79426c74dd91d075a3e2c85c6f65dde122637dbc09e250a192141d0107a8e2f",
2498
+ "language": "Python",
2499
+ "lines": 21,
2500
+ "truncated": false,
2501
+ "block": 3,
2502
+ "row": 18469
2503
+ },
2504
+ {
2505
+ "path": "tests/distributions/test_gamma.py",
2506
+ "sha256": "6787c53a0252be8a3f3d0b77a7c9da4f82d8f411b33921fbceb73530269a540b",
2507
+ "language": "Python",
2508
+ "lines": 154,
2509
+ "truncated": false,
2510
+ "block": 3,
2511
+ "row": 23311
2512
+ },
2513
+ {
2514
+ "path": "tests/distributions/test_lognormal.py",
2515
+ "sha256": "705acba5203479b6429b49730a669784105dd479b52c69d4178f73ae9a8914d1",
2516
+ "language": "Python",
2517
+ "lines": 146,
2518
+ "truncated": false,
2519
+ "block": 3,
2520
+ "row": 22840
2521
+ },
2522
+ {
2523
+ "path": "tests/distributions/test_negative_binomial.py",
2524
+ "sha256": "2d3821b7a6f0fc574498b562252a931ee2ba62ce296ddf831c079ee1663b1755",
2525
+ "language": "Python",
2526
+ "lines": 230,
2527
+ "truncated": false,
2528
+ "block": 3,
2529
+ "row": 25148
2530
+ },
2531
+ {
2532
+ "path": "tests/external/cellassign/test_model_cellassign.py",
2533
+ "sha256": "4ba144802c56804386352ee897c215cf71067399d202ee25c8e37214b60a0a29",
2534
+ "language": "Python",
2535
+ "lines": 61,
2536
+ "truncated": false,
2537
+ "block": 3,
2538
+ "row": 19762
2539
+ },
2540
+ {
2541
+ "path": "tests/external/contrastivevi/test_contrastive_dataloaders.py",
2542
+ "sha256": "89aedea28e4d08788fc595ef162bd6196a80a1db1b8c0b6203abc926b8950af1",
2543
+ "language": "Python",
2544
+ "lines": 54,
2545
+ "truncated": false,
2546
+ "block": 3,
2547
+ "row": 20378
2548
+ },
2549
+ {
2550
+ "path": "tests/external/contrastivevi/test_contrastive_datasplitter.py",
2551
+ "sha256": "748003cab2fbcc3d9bc3cd535421cda1fa4d7ca4c4acba67a907518d48979bce",
2552
+ "language": "Python",
2553
+ "lines": 158,
2554
+ "truncated": false,
2555
+ "block": 3,
2556
+ "row": 23827
2557
+ },
2558
+ {
2559
+ "path": "tests/external/contrastivevi/test_contrastivevae.py",
2560
+ "sha256": "e284d083c3f998afdbdb216336d35033d3905ea985d2e4997086320643cc57b7",
2561
+ "language": "Python",
2562
+ "lines": 458,
2563
+ "truncated": false,
2564
+ "block": 3,
2565
+ "row": 26806
2566
+ },
2567
+ {
2568
+ "path": "tests/external/contrastivevi/test_contrastivevi.py",
2569
+ "sha256": "e4959c0c4e3cefece766f04d9e802e4b1f1a5be665b3d60d1d72281665e19242",
2570
+ "language": "Python",
2571
+ "lines": 165,
2572
+ "truncated": false,
2573
+ "block": 3,
2574
+ "row": 23858
2575
+ },
2576
+ {
2577
+ "path": "tests/external/cytovi/test_cytovi.py",
2578
+ "sha256": "a1d1acd78c658d5803880005cfec10f63f3f904b2262854da5a255d92fb0d5aa",
2579
+ "language": "Python",
2580
+ "lines": 301,
2581
+ "truncated": false,
2582
+ "block": 3,
2583
+ "row": 24995
2584
+ },
2585
+ {
2586
+ "path": "tests/external/decipher/test_decipher.py",
2587
+ "sha256": "abbfe907450dc7a47cf880a262fdf0510ff09d089d6b8be8cbb5a41c05be4b56",
2588
+ "language": "Python",
2589
+ "lines": 135,
2590
+ "truncated": false,
2591
+ "block": 3,
2592
+ "row": 22218
2593
+ },
2594
+ {
2595
+ "path": "tests/external/diagvi/test_diagvi.py",
2596
+ "sha256": "c4775766a78fdeadc7aa365c3fc917f6b771996a139b8ed3e6c84941fa952dc0",
2597
+ "language": "Python",
2598
+ "lines": 1680,
2599
+ "truncated": false,
2600
+ "block": 3,
2601
+ "row": 28041
2602
+ },
2603
+ {
2604
+ "path": "tests/external/drvi/test_drvi.py",
2605
+ "sha256": "c3789014f6a14bf45fb0c6c364038c7c715a74343fdf53503789d17d4505c827",
2606
+ "language": "Python",
2607
+ "lines": 641,
2608
+ "truncated": false,
2609
+ "block": 3,
2610
+ "row": 27422
2611
+ },
2612
+ {
2613
+ "path": "tests/external/gimvi/test_gimvi.py",
2614
+ "sha256": "eb6ace106ad9738217eb00599888f252275572154b83ab5c105b62a3ec5b5fd3",
2615
+ "language": "Python",
2616
+ "lines": 232,
2617
+ "truncated": false,
2618
+ "block": 3,
2619
+ "row": 24318
2620
+ },
2621
+ {
2622
+ "path": "tests/external/joint_embedding_scvi/test_joint_embedding_scvi.py",
2623
+ "sha256": "01b8c8e46a694ae80926cac0e72e769655dc25648d6f66f61265809da4ff5de1",
2624
+ "language": "Python",
2625
+ "lines": 151,
2626
+ "truncated": false,
2627
+ "block": 3,
2628
+ "row": 23190
2629
+ },
2630
+ {
2631
+ "path": "tests/external/joint_embedding_scvi/test_joint_embedding_utils.py",
2632
+ "sha256": "a4e86ef5cf0aa788d4d3eeb482d91f6f022011ddb3184f388acddff74d123197",
2633
+ "language": "Python",
2634
+ "lines": 61,
2635
+ "truncated": false,
2636
+ "block": 3,
2637
+ "row": 20197
2638
+ },
2639
+ {
2640
+ "path": "tests/external/methylvi/test_methylanvi.py",
2641
+ "sha256": "d0240f5f8d815403392ca877d009e27ce4c7ba9278a3815695c141ed3343e91a",
2642
+ "language": "Python",
2643
+ "lines": 45,
2644
+ "truncated": false,
2645
+ "block": 3,
2646
+ "row": 19539
2647
+ },
2648
+ {
2649
+ "path": "tests/external/methylvi/test_methylvi.py",
2650
+ "sha256": "b518dbeabf2cf4289c94a606efa7c4c6c66d10e0a50709b5c6c57bef824905b5",
2651
+ "language": "Python",
2652
+ "lines": 62,
2653
+ "truncated": false,
2654
+ "block": 3,
2655
+ "row": 20078
2656
+ },
2657
+ {
2658
+ "path": "tests/external/mrvi/test_mrvi_components.py",
2659
+ "sha256": "62525138cc018564302c00827ac8d7dc9e87b93873d5801529d65b3a1dbecb1d",
2660
+ "language": "Python",
2661
+ "lines": 82,
2662
+ "truncated": false,
2663
+ "block": 3,
2664
+ "row": 20354
2665
+ },
2666
+ {
2667
+ "path": "tests/external/mrvi/test_mrvi_model.py",
2668
+ "sha256": "5cee68db418046ce28f82a4d43e13be4e31bf7e709c037fce4f4b46a62d8f632",
2669
+ "language": "Python",
2670
+ "lines": 375,
2671
+ "truncated": false,
2672
+ "block": 3,
2673
+ "row": 26091
2674
+ },
2675
+ {
2676
+ "path": "tests/external/poissonvi/test_poissonvi.py",
2677
+ "sha256": "5625a9f5bb63fe34e3708be2c0977396967e62a9952f72675ed2e76b7ea3859a",
2678
+ "language": "Python",
2679
+ "lines": 85,
2680
+ "truncated": false,
2681
+ "block": 3,
2682
+ "row": 21462
2683
+ },
2684
+ {
2685
+ "path": "tests/external/resolvi/test_resolvi.py",
2686
+ "sha256": "9b111861ab8fc458254a1c499cc4e223994182fe48da7105cc034e435f51120b",
2687
+ "language": "Python",
2688
+ "lines": 227,
2689
+ "truncated": false,
2690
+ "block": 3,
2691
+ "row": 24839
2692
+ },
2693
+ {
2694
+ "path": "tests/external/scar/test_scar.py",
2695
+ "sha256": "d94aa63e487575394ffe8d958bf0d5abf07240b0ae09bba319a572e828784c40",
2696
+ "language": "Python",
2697
+ "lines": 27,
2698
+ "truncated": false,
2699
+ "block": 3,
2700
+ "row": 18764
2701
+ },
2702
+ {
2703
+ "path": "tests/external/scbasset/test_scbasset.py",
2704
+ "sha256": "ee1c9caaab1a567f0ce92d76c8be1cb98e8e8bef0897cb993143713ae9c5c32d",
2705
+ "language": "Python",
2706
+ "lines": 40,
2707
+ "truncated": false,
2708
+ "block": 3,
2709
+ "row": 19024
2710
+ },
2711
+ {
2712
+ "path": "tests/external/scviva/test_scviva.py",
2713
+ "sha256": "5da44426c202bb7324f49ab4f9e6cb0cafac4e22a219a49fa232643d54bca3d7",
2714
+ "language": "Python",
2715
+ "lines": 478,
2716
+ "truncated": false,
2717
+ "block": 3,
2718
+ "row": 26143
2719
+ },
2720
+ {
2721
+ "path": "tests/external/solo/test_solo.py",
2722
+ "sha256": "b8f1bc187de60baedfc89fd1e1a6c4c91bdaa10b343f79d55229fe62a47d2b8f",
2723
+ "language": "Python",
2724
+ "lines": 113,
2725
+ "truncated": false,
2726
+ "block": 3,
2727
+ "row": 21864
2728
+ },
2729
+ {
2730
+ "path": "tests/external/stereoscope/test_stereoscope.py",
2731
+ "sha256": "2f49850e6cfff0acfaa480fa1e6aff4190a95776cb132363e006c0d7259d7bcd",
2732
+ "language": "Python",
2733
+ "lines": 42,
2734
+ "truncated": false,
2735
+ "block": 3,
2736
+ "row": 19215
2737
+ },
2738
+ {
2739
+ "path": "tests/external/sysvi/test_sysvi.py",
2740
+ "sha256": "3fbc20adb066e083eb8f06c0b258b8c9fbcc6dad689f25a9b3328587f51d4ab1",
2741
+ "language": "Python",
2742
+ "lines": 343,
2743
+ "truncated": false,
2744
+ "block": 3,
2745
+ "row": 25572
2746
+ },
2747
+ {
2748
+ "path": "tests/external/tangram/test_tangram.py",
2749
+ "sha256": "511fbc83198db1a7c54c83f6003f01725dc691167f38afe56d5da44e509e1039",
2750
+ "language": "Python",
2751
+ "lines": 95,
2752
+ "truncated": false,
2753
+ "block": 3,
2754
+ "row": 21059
2755
+ },
2756
+ {
2757
+ "path": "tests/external/totalanvi/test_totalanvi.py",
2758
+ "sha256": "6934c82eb55c522e1116da944917193b8d850c08306cd35f4a80e07d8c200142",
2759
+ "language": "Python",
2760
+ "lines": 517,
2761
+ "truncated": false,
2762
+ "block": 3,
2763
+ "row": 27012
2764
+ },
2765
+ {
2766
+ "path": "tests/external/velovi/test_velovi.py",
2767
+ "sha256": "8a2db7e5439ec485d9b0ae56456e3d064be51dbc812a74078055b79584c4faae",
2768
+ "language": "Python",
2769
+ "lines": 65,
2770
+ "truncated": false,
2771
+ "block": 3,
2772
+ "row": 20491
2773
+ },
2774
+ {
2775
+ "path": "tests/external/vivs/test_vivs.py",
2776
+ "sha256": "998a534f98a127a8dcd77aff60f13813cb9000390d7de232ce2f6281f9fc22db",
2777
+ "language": "Python",
2778
+ "lines": 467,
2779
+ "truncated": false,
2780
+ "block": 3,
2781
+ "row": 26822
2782
+ },
2783
+ {
2784
+ "path": "tests/hub/test_hub_metadata.py",
2785
+ "sha256": "a57960382e63aee00b3ef9525828569a02c9c7a23197786a5974f058519161e9",
2786
+ "language": "Python",
2787
+ "lines": 196,
2788
+ "truncated": false,
2789
+ "block": 3,
2790
+ "row": 23793
2791
+ },
2792
+ {
2793
+ "path": "tests/hub/test_hub_model.py",
2794
+ "sha256": "64a31a8c8dc280ae6868dec3f75a64db312926063742f8f6c5cc4dddb42915f1",
2795
+ "language": "Python",
2796
+ "lines": 399,
2797
+ "truncated": false,
2798
+ "block": 3,
2799
+ "row": 26281
2800
+ },
2801
+ {
2802
+ "path": "tests/hub/test_url.py",
2803
+ "sha256": "29f84feb2c193e9e9e101be02db7a7c76e09d1631306cbca95a7a693dd3c5331",
2804
+ "language": "Python",
2805
+ "lines": 49,
2806
+ "truncated": false,
2807
+ "block": 3,
2808
+ "row": 19270
2809
+ },
2810
+ {
2811
+ "path": "tests/model/base/test_base_model.py",
2812
+ "sha256": "003f71aaf14929b39157bf53c3441adc1251defdbf042cdcf4535101c0bd9ef3",
2813
+ "language": "Python",
2814
+ "lines": 90,
2815
+ "truncated": false,
2816
+ "block": 3,
2817
+ "row": 21759
2818
+ },
2819
+ {
2820
+ "path": "tests/model/base/test_rnamixin.py",
2821
+ "sha256": "363491f7f10b3f672d2fe4d8b3f882bdd3036bd3d689c8aa1445b1dcfb4c1aca",
2822
+ "language": "Python",
2823
+ "lines": 33,
2824
+ "truncated": false,
2825
+ "block": 3,
2826
+ "row": 19325
2827
+ },
2828
+ {
2829
+ "path": "tests/model/test_amortizedlda.py",
2830
+ "sha256": "8004322da26bbb0bfd7023ca35008a435787f7799248a04a1b6436b6e7db0893",
2831
+ "language": "Python",
2832
+ "lines": 124,
2833
+ "truncated": false,
2834
+ "block": 3,
2835
+ "row": 22258
2836
+ },
2837
+ {
2838
+ "path": "tests/model/test_autozi.py",
2839
+ "sha256": "f51adf3903e04ca031cb1222527cf16542a94286ad6b0880ba1f35219d8ce71a",
2840
+ "language": "Python",
2841
+ "lines": 167,
2842
+ "truncated": false,
2843
+ "block": 3,
2844
+ "row": 23833
2845
+ },
2846
+ {
2847
+ "path": "tests/model/test_condscvi.py",
2848
+ "sha256": "c68f871079711e01e7e9a0f92e86d7536020523cca3d75e8fef96e6739f64f57",
2849
+ "language": "Python",
2850
+ "lines": 81,
2851
+ "truncated": false,
2852
+ "block": 3,
2853
+ "row": 21161
2854
+ },
2855
+ {
2856
+ "path": "tests/model/test_destvi.py",
2857
+ "sha256": "995bbac9c5259bf6be739b27b29afc4f3cd7cc042beadb78c570623a46715c6c",
2858
+ "language": "Python",
2859
+ "lines": 194,
2860
+ "truncated": false,
2861
+ "block": 3,
2862
+ "row": 24411
2863
+ },
2864
+ {
2865
+ "path": "tests/model/test_differential.py",
2866
+ "sha256": "be7ffea9bdcc4b2546e664881d8b63f8ef0db2fee871a19ad1dfa0d3c60314a7",
2867
+ "language": "Python",
2868
+ "lines": 163,
2869
+ "truncated": false,
2870
+ "block": 3,
2871
+ "row": 22775
2872
+ },
2873
+ {
2874
+ "path": "tests/model/test_differential_abundance.py",
2875
+ "sha256": "99c56c338b58ab11cf85b296070c8062497ff9c3c2b56a07cdbfdab3af8229ba",
2876
+ "language": "Python",
2877
+ "lines": 174,
2878
+ "truncated": false,
2879
+ "block": 3,
2880
+ "row": 23619
2881
+ },
2882
+ {
2883
+ "path": "tests/model/test_docstrings.py",
2884
+ "sha256": "bc13ec884d0f45144748b0b1acb3d651934110582674bfff3c38ba13d25dc945",
2885
+ "language": "Python",
2886
+ "lines": 38,
2887
+ "truncated": false,
2888
+ "block": 3,
2889
+ "row": 19544
2890
+ },
2891
+ {
2892
+ "path": "tests/model/test_linear_scvi.py",
2893
+ "sha256": "0002c30888fa1dd3a0cacde85610509c2ca735d2feb560d39378b1d736f7d85e",
2894
+ "language": "Python",
2895
+ "lines": 157,
2896
+ "truncated": false,
2897
+ "block": 3,
2898
+ "row": 23553
2899
+ },
2900
+ {
2901
+ "path": "tests/model/test_mlxscvi.py",
2902
+ "sha256": "8e8c215b9f352a78b685331589a4fdc5e1239d1eb48366ccef54ac09c9477b50",
2903
+ "language": "Python",
2904
+ "lines": 224,
2905
+ "truncated": false,
2906
+ "block": 3,
2907
+ "row": 24442
2908
+ },
2909
+ {
2910
+ "path": "tests/model/test_models_with_minified_data.py",
2911
+ "sha256": "bda8ae994dc87d8b341e2ecda23a915526a74c9a0b53fd65e02d1cb76a8bc77e",
2912
+ "language": "Python",
2913
+ "lines": 546,
2914
+ "truncated": false,
2915
+ "block": 3,
2916
+ "row": 27064
2917
+ },
2918
+ {
2919
+ "path": "tests/model/test_models_with_mudata_minified_data.py",
2920
+ "sha256": "9a82e9d4da0506fa89413eb2f33af653b8379d97a2515b654e94636170c8711e",
2921
+ "language": "Python",
2922
+ "lines": 512,
2923
+ "truncated": false,
2924
+ "block": 3,
2925
+ "row": 27025
2926
+ },
2927
+ {
2928
+ "path": "tests/model/test_multigpu.py",
2929
+ "sha256": "047241ceb99d0e6e65c967304f29ba3cd60bd533ea3efbd6f15efc21f7a3fea9",
2930
+ "language": "Python",
2931
+ "lines": 338,
2932
+ "truncated": false,
2933
+ "block": 3,
2934
+ "row": 25050
2935
+ },
2936
+ {
2937
+ "path": "tests/model/test_multivi.py",
2938
+ "sha256": "3984e4a23cbed7f785e6195a88c54caab925e70142e6c5e906af6e22a6767089",
2939
+ "language": "Python",
2940
+ "lines": 609,
2941
+ "truncated": false,
2942
+ "block": 3,
2943
+ "row": 27187
2944
+ },
2945
+ {
2946
+ "path": "tests/model/test_peakvi.py",
2947
+ "sha256": "67dfd5053e50e2029be9837626fa2537b7410cea4ce3d0e480fafe59f8e70ae5",
2948
+ "language": "Python",
2949
+ "lines": 238,
2950
+ "truncated": false,
2951
+ "block": 3,
2952
+ "row": 24616
2953
+ },
2954
+ {
2955
+ "path": "tests/model/test_pyro.py",
2956
+ "sha256": "3b40bf62ccd6d6e3db6b06c5a6c40b387f92b682336edeadc0435bbb65aefa82",
2957
+ "language": "Python",
2958
+ "lines": 562,
2959
+ "truncated": false,
2960
+ "block": 3,
2961
+ "row": 26986
2962
+ },
2963
+ {
2964
+ "path": "tests/model/test_scanvi.py",
2965
+ "sha256": "bed49c09e03f64341105bdf95487df14fc7356a68f645d2ba8bc43c6fa30978d",
2966
+ "language": "Python",
2967
+ "lines": 741,
2968
+ "truncated": false,
2969
+ "block": 3,
2970
+ "row": 27501
2971
+ },
2972
+ {
2973
+ "path": "tests/model/test_scvi.py",
2974
+ "sha256": "393a9cc418178b6760323511a28c39b412db57fa46656c4a4138c7a8b856ac9b",
2975
+ "language": "Python",
2976
+ "lines": 1716,
2977
+ "truncated": false,
2978
+ "block": 4,
2979
+ "row": 0
2980
+ },
2981
+ {
2982
+ "path": "tests/model/test_totalvi.py",
2983
+ "sha256": "4b7f799d9f2a24529315defbedd6e8e17d7e54ac5fcffe812ce353c755dfd452",
2984
+ "language": "Python",
2985
+ "lines": 831,
2986
+ "truncated": false,
2987
+ "block": 3,
2988
+ "row": 27598
2989
+ },
2990
+ {
2991
+ "path": "tests/model/test_utils.py",
2992
+ "sha256": "af83e81e5433904477bf8d5ee20926cfd85861b3b41fa996b132bcfdb6e66672",
2993
+ "language": "Python",
2994
+ "lines": 33,
2995
+ "truncated": false,
2996
+ "block": 3,
2997
+ "row": 20013
2998
+ },
2999
+ {
3000
+ "path": "tests/module/test_scanvae.py",
3001
+ "sha256": "58aa23e548259b8c4e72f7ff1c813b0ad83168fbbef5be0394f92a60ba84efc5",
3002
+ "language": "Python",
3003
+ "lines": 41,
3004
+ "truncated": false,
3005
+ "block": 3,
3006
+ "row": 19438
3007
+ },
3008
+ {
3009
+ "path": "tests/module/test_vae.py",
3010
+ "sha256": "5f0778055012ef659d36a289dadd0391e6b4cdedbb2b7ac35c35486a233cd3ae",
3011
+ "language": "Python",
3012
+ "lines": 71,
3013
+ "truncated": false,
3014
+ "block": 3,
3015
+ "row": 20768
3016
+ },
3017
+ {
3018
+ "path": "tests/nn/test_embedding.py",
3019
+ "sha256": "54dc36107d06636d829d21ae0ad345a80e3aeae4982fda3f736100e252c73329",
3020
+ "language": "Python",
3021
+ "lines": 76,
3022
+ "truncated": false,
3023
+ "block": 3,
3024
+ "row": 21078
3025
+ },
3026
+ {
3027
+ "path": "tests/nn/test_fclayers.py",
3028
+ "sha256": "203ded2bda25edf64162019f862d8904970cfa4fb4b581442ef5cfd12baabdd4",
3029
+ "language": "Python",
3030
+ "lines": 245,
3031
+ "truncated": false,
3032
+ "block": 3,
3033
+ "row": 24872
3034
+ },
3035
+ {
3036
+ "path": "tests/test_warnings.py",
3037
+ "sha256": "1a42e02d1191d23f393b2463d2205c3597c86ddd8d790ef934a5339321b19fdd",
3038
+ "language": "Python",
3039
+ "lines": 46,
3040
+ "truncated": false,
3041
+ "block": 3,
3042
+ "row": 19698
3043
+ },
3044
+ {
3045
+ "path": "tests/train/test_callbacks.py",
3046
+ "sha256": "646012a2d70644c3618ad4ce84bd807109778c1ddf7a597826e0cac453c76b99",
3047
+ "language": "Python",
3048
+ "lines": 267,
3049
+ "truncated": false,
3050
+ "block": 3,
3051
+ "row": 24720
3052
+ },
3053
+ {
3054
+ "path": "tests/train/test_config.py",
3055
+ "sha256": "4c1c7363b09ae61b105f313b528e7b04a4a2ef5ab5918f05c94945d8bdcc7205",
3056
+ "language": "Python",
3057
+ "lines": 44,
3058
+ "truncated": false,
3059
+ "block": 3,
3060
+ "row": 19256
3061
+ },
3062
+ {
3063
+ "path": "tests/train/test_trainingplans.py",
3064
+ "sha256": "c1b338ff624c598282d73a7815bb723f128e45e56ae4d0b91d764827280be8f0",
3065
+ "language": "Python",
3066
+ "lines": 212,
3067
+ "truncated": false,
3068
+ "block": 3,
3069
+ "row": 24321
3070
+ }
3071
+ ]
3072
+ }
manifests/fe/github.com__yingqihao2022__panda.json ADDED
@@ -0,0 +1,75 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/yingqihao2022/panda",
4
+ "url": "https://github.com/yingqihao2022/PANDA",
5
+ "host": "github.com",
6
+ "commit": "40e00a386b65d617b056bc332bb112c78fb059d2",
7
+ "license": "MIT",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "3e640230f750667708933c6a4dd470d3d62489cc9a7f2945b6704c99bae49eb0",
14
+ "language": "License",
15
+ "lines": 21,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 7957
19
+ },
20
+ {
21
+ "path": "README.md",
22
+ "sha256": "d9bfbe4598f135b58f5cff193e79eed10995ca85365bca451312b11e04d0cea6",
23
+ "language": "Text",
24
+ "lines": 71,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 2359
28
+ },
29
+ {
30
+ "path": "fdataset.py",
31
+ "sha256": "18d8cd34eda1a662b586b6cc437b17a2eb4a81788c2c894777b169072d2d9578",
32
+ "language": "Python",
33
+ "lines": 61,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 20356
37
+ },
38
+ {
39
+ "path": "inference.py",
40
+ "sha256": "1c948f733cbe736d8a070679207ae3d5d7d067cdb1793e2ca585b24ebf66bae7",
41
+ "language": "Python",
42
+ "lines": 44,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 19612
46
+ },
47
+ {
48
+ "path": "preprocess.py",
49
+ "sha256": "9f8b4c3fe4148e480027f79b3d98e804eb982cd12dad220610ffc798d9be3d7c",
50
+ "language": "Python",
51
+ "lines": 112,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 22199
55
+ },
56
+ {
57
+ "path": "sfcn.py",
58
+ "sha256": "6b0fb096afec83f03bc09eeadf0c1c6bfa53716cea201e39dde177c16e5e693b",
59
+ "language": "Python",
60
+ "lines": 80,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 21630
64
+ },
65
+ {
66
+ "path": "train.py",
67
+ "sha256": "96b4faa7c6ce2a180ba3b5014e2e2ced1b96e405553325244a9cb9d943533066",
68
+ "language": "Python",
69
+ "lines": 130,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 22956
73
+ }
74
+ ]
75
+ }
manifests/fe/zenodo__16809359.json ADDED
@@ -0,0 +1,255 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:16809359",
4
+ "url": "https://doi.org/10.5281/zenodo.16809359",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "CC-BY-4.0",
8
+ "license_confirmed_by": "license of the archive's record",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "README.md",
13
+ "sha256": "534d731401ba8efffd215ce90b0eb057d888d50fdd0eb1d2c395ae57bdcf8faf",
14
+ "language": "Text",
15
+ "lines": 57,
16
+ "truncated": false,
17
+ "block": 4,
18
+ "row": 2390
19
+ },
20
+ {
21
+ "path": "SimplePolynomial.ipynb",
22
+ "sha256": "b2e089e09d4fce10b450e45403c7295ea682f01471974ea2429de1e7df4fb5c4",
23
+ "language": "Jupyter",
24
+ "lines": 349,
25
+ "truncated": false,
26
+ "block": 3,
27
+ "row": 7641
28
+ },
29
+ {
30
+ "path": "gcn_task/STONEDanalysis.ipynb",
31
+ "sha256": "60011db547123a80640cc8f13d4a3d8024904710c9700b99105d7f5536a972bb",
32
+ "language": "Jupyter",
33
+ "lines": 538,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 7710
37
+ },
38
+ {
39
+ "path": "gcn_task/adversarial_eval.py",
40
+ "sha256": "c036781f911cc77d86ff0a993b2d92f7312b4ee2d4a3fbca140b64d60fe18b35",
41
+ "language": "Python",
42
+ "lines": 411,
43
+ "truncated": false,
44
+ "block": 3,
45
+ "row": 26466
46
+ },
47
+ {
48
+ "path": "gcn_task/dglgcn.py",
49
+ "sha256": "8cf3fd7c2c8bcb8c9e613768972996922e061b6e1419a9647b7eb93c61f02138",
50
+ "language": "Python",
51
+ "lines": 1122,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 27899
55
+ },
56
+ {
57
+ "path": "gcn_task/gcn_results/postprocess_stuff/adversarial_postprocess.ipynb",
58
+ "sha256": "82e2c3c3ed850aa4c419465da6813c52a069430bf26457d1ad6e6cc468135cb4",
59
+ "language": "Jupyter",
60
+ "lines": 359,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 7643
64
+ },
65
+ {
66
+ "path": "gcn_task/gcn_results/postprocess_stuff/adversarial_training_curves.py",
67
+ "sha256": "acdf505c6209e0932c1ffa3522c8ff2791e90957e5f996fd533fe9e734ab9da5",
68
+ "language": "Python",
69
+ "lines": 118,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 22471
73
+ },
74
+ {
75
+ "path": "gcn_task/gcn_results/postprocess_stuff/correlation_tables.ipynb",
76
+ "sha256": "d5e7dff53cc86382b92e1b899a41d81690f4d2ec60e6f0c9c64c0dc5888d01b4",
77
+ "language": "Jupyter",
78
+ "lines": 157,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 7344
82
+ },
83
+ {
84
+ "path": "gcn_task/gcn_results/postprocess_stuff/main_plots.ipynb",
85
+ "sha256": "22af51de8189f5c032fca4a7ff1265f1b8925bfc072e192b2d1e6df6f6230beb",
86
+ "language": "Jupyter",
87
+ "lines": 472,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 7729
91
+ },
92
+ {
93
+ "path": "gcn_task/gcn_results/postprocess_stuff/statistical_tests.ipynb",
94
+ "sha256": "1619bae706053b48560c935a8795989f6984cefd544c6a86c88fc0caec8edce4",
95
+ "language": "Jupyter",
96
+ "lines": 383,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 7623
100
+ },
101
+ {
102
+ "path": "gcn_task/gcn_results/postprocess_stuff/tradeoff_analysis.ipynb",
103
+ "sha256": "f713ac08c6b7dad16a391e26736b75753732c3a7a5be85e99dae69f390936b20",
104
+ "language": "Jupyter",
105
+ "lines": 295,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 7593
109
+ },
110
+ {
111
+ "path": "gcn_task/gcn_results/postprocess_stuff/training_curves_n_parity_plots.ipynb",
112
+ "sha256": "dededb3215a427022113d82f9c3793d63695fdc27709210a2d87d93545ed123c",
113
+ "language": "Jupyter",
114
+ "lines": 209,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 7487
118
+ },
119
+ {
120
+ "path": "gcn_task/omission_gcn.ipynb",
121
+ "sha256": "b66dee65bb2c8c787597049f6a0296f60bbc8482faa3b392b3cd99a0892de3a3",
122
+ "language": "Jupyter",
123
+ "lines": 198,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 7423
127
+ },
128
+ {
129
+ "path": "gcn_task/papermill_run.py",
130
+ "sha256": "6a45c6f905b7076c219155581fb1e54f605d6343f8a4c2887eec6f1ea897112a",
131
+ "language": "Python",
132
+ "lines": 52,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 20294
136
+ },
137
+ {
138
+ "path": "gcn_task/xnoise_gcn.ipynb",
139
+ "sha256": "4fdaa4a349d25a0b1119a545079ba1bda88496832deba569ad02d7cbe540f521",
140
+ "language": "Jupyter",
141
+ "lines": 229,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 7457
145
+ },
146
+ {
147
+ "path": "gcn_task/ynoise_gcn.ipynb",
148
+ "sha256": "18ed6c30e736be74fb65653e0ef6c91a9e1cd693acd46693249a49b78554be4f",
149
+ "language": "Jupyter",
150
+ "lines": 201,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 7435
154
+ },
155
+ {
156
+ "path": "mlp_task/censor_methods.py",
157
+ "sha256": "2cf949e6067f88384b46c836c8a5f028f22149bfcdae625b04fde38344ed26d6",
158
+ "language": "Python",
159
+ "lines": 174,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 23970
163
+ },
164
+ {
165
+ "path": "mlp_task/mlp_fxns.py",
166
+ "sha256": "35edf10bf48a95d48ca4684616c2c69b476f4e1bdf31ab9d3082bd116f6fc8bf",
167
+ "language": "Python",
168
+ "lines": 379,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 26159
172
+ },
173
+ {
174
+ "path": "mlp_task/mlp_quick_comparison_run.ipynb",
175
+ "sha256": "08105eacba4d450de70bddf7d8f2e4d263bb338bc749a5353f494bf87676c49e",
176
+ "language": "Jupyter",
177
+ "lines": 587,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 7747
181
+ },
182
+ {
183
+ "path": "mlp_task/mlp_results/mlp_correlation_tables.ipynb",
184
+ "sha256": "aeb7f9d5b17df940fb62e13092b7879f5f67bd4ac672000b74a17b6b07878dd1",
185
+ "language": "Jupyter",
186
+ "lines": 158,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 7357
190
+ },
191
+ {
192
+ "path": "mlp_task/mlp_results/mlp_main_plots.ipynb",
193
+ "sha256": "1825b51a82ca467878ee3639c6ff5949d5ee17ea4fb77a48c6d8b2b413fbc5a0",
194
+ "language": "Jupyter",
195
+ "lines": 549,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 7753
199
+ },
200
+ {
201
+ "path": "mlp_task/mlp_results/statistical_tests.ipynb",
202
+ "sha256": "7b3d1046c95c1db8aaeec91f7e179262bb61f80c52015910502ddc894da0dfc7",
203
+ "language": "Jupyter",
204
+ "lines": 460,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 7681
208
+ },
209
+ {
210
+ "path": "mlp_task/omit_mlp.ipynb",
211
+ "sha256": "d97f1f40f24a9015b9fd32b970a146fd11333c27b934748bbccbc3af26467460",
212
+ "language": "Jupyter",
213
+ "lines": 248,
214
+ "truncated": false,
215
+ "block": 3,
216
+ "row": 7522
217
+ },
218
+ {
219
+ "path": "mlp_task/papermill_run.py",
220
+ "sha256": "79382a79544a4b92b5311c4065df275e9152752be828e796cf60839c7ee39b78",
221
+ "language": "Python",
222
+ "lines": 44,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 19905
226
+ },
227
+ {
228
+ "path": "mlp_task/plot_fxns.py",
229
+ "sha256": "dd37bee91dc6e7cb9e3275dc29e96d58eb32de8bb7c37ce71c120d16958ce675",
230
+ "language": "Python",
231
+ "lines": 80,
232
+ "truncated": false,
233
+ "block": 3,
234
+ "row": 21440
235
+ },
236
+ {
237
+ "path": "mlp_task/xnoise_mlp.ipynb",
238
+ "sha256": "4db8e67cef58a1b0d50dff2b0b65be7a7cf9fb3050e960a847b0f36bc9d0ddfb",
239
+ "language": "Jupyter",
240
+ "lines": 202,
241
+ "truncated": false,
242
+ "block": 3,
243
+ "row": 7426
244
+ },
245
+ {
246
+ "path": "mlp_task/ynoise_mlp.ipynb",
247
+ "sha256": "076e388b37e919dbc999bd177599e01d6ca6335b69808a406c25e3db817e57e2",
248
+ "language": "Jupyter",
249
+ "lines": 196,
250
+ "truncated": false,
251
+ "block": 3,
252
+ "row": 7421
253
+ }
254
+ ]
255
+ }
manifests/ff/github.com__precimed__python_convert.json ADDED
@@ -0,0 +1,309 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "github.com/precimed/python_convert",
4
+ "url": "https://github.com/precimed/python_convert/",
5
+ "host": "github.com",
6
+ "commit": "e46ebdfafd495c1420c7f8a4740a0da75c94d84d",
7
+ "license": "GPL-3.0",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "LICENSE",
13
+ "sha256": "782ea738efeda1c64b6f7f034cada3b809a3e44c03e16fcef7cf9d9d81a86028",
14
+ "language": "License",
15
+ "lines": 219,
16
+ "truncated": false,
17
+ "block": 3,
18
+ "row": 8167
19
+ },
20
+ {
21
+ "path": "Liftover_SNP.py",
22
+ "sha256": "36255d6e646bfdd905328248ceccc23cf2274afd71d0809194c54044763cd803",
23
+ "language": "Python",
24
+ "lines": 469,
25
+ "truncated": false,
26
+ "block": 3,
27
+ "row": 27186
28
+ },
29
+ {
30
+ "path": "PLINK_file_Utils.py",
31
+ "sha256": "f1f69749addb545af65146c33c981e2f0eda9345b559cb851668c2d037345c4a",
32
+ "language": "Python",
33
+ "lines": 96,
34
+ "truncated": false,
35
+ "block": 3,
36
+ "row": 21887
37
+ },
38
+ {
39
+ "path": "README.md",
40
+ "sha256": "d50ebe7bedf993a49b13c595292416931a5b7effe60dd306e981c5227a53321b",
41
+ "language": "Text",
42
+ "lines": 159,
43
+ "truncated": false,
44
+ "block": 4,
45
+ "row": 2628
46
+ },
47
+ {
48
+ "path": "annotation.py",
49
+ "sha256": "994b47578331cb2b3002872777a046c202f4efeae61d0be0e9503c136e2dc31b",
50
+ "language": "Python",
51
+ "lines": 197,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 25035
55
+ },
56
+ {
57
+ "path": "aud_meta_qq_lambdas.ipynb",
58
+ "sha256": "5b18d597df31d6fc3ab51bfa9b62ba742c3f49cea62451945663d319dbcef647",
59
+ "language": "Jupyter",
60
+ "lines": 97,
61
+ "truncated": false,
62
+ "block": 3,
63
+ "row": 7221
64
+ },
65
+ {
66
+ "path": "convert_cleansumstats_output_to_mixer_format.py",
67
+ "sha256": "4edf05d3ea683e48e322b844de5d78d0dd988ae1148355ad97112adf0af324d2",
68
+ "language": "Python",
69
+ "lines": 36,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 20008
73
+ },
74
+ {
75
+ "path": "fdrmat2csv.py",
76
+ "sha256": "812051d9deb614c136248b7c4fb5e653b6fde062100cfb799d82db186ed0ffa6",
77
+ "language": "Python",
78
+ "lines": 51,
79
+ "truncated": false,
80
+ "block": 3,
81
+ "row": 19748
82
+ },
83
+ {
84
+ "path": "lift_rs_numbers.py",
85
+ "sha256": "709bf4a20882140979beb87f8c73643df995b349ceab7f703b0d0f0c4acbd3e3",
86
+ "language": "Python",
87
+ "lines": 63,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 20795
91
+ },
92
+ {
93
+ "path": "make_ld_matrix/genotypes2ref.py",
94
+ "sha256": "86fd63b30fe992eb8b00fd65462249b15620563ce1eb6d259b981c01b9bf1161",
95
+ "language": "Python",
96
+ "lines": 71,
97
+ "truncated": false,
98
+ "block": 3,
99
+ "row": 21586
100
+ },
101
+ {
102
+ "path": "make_ld_matrix/make_ld_matrix.py",
103
+ "sha256": "2eff034e3e2e4e747f10ab2e43383c8f9be01d3e9e06cbd3bfcdd0f3c8c5b12c",
104
+ "language": "Python",
105
+ "lines": 136,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 24181
109
+ },
110
+ {
111
+ "path": "make_ld_matrix/make_maf_vector.py",
112
+ "sha256": "8bd731701f16b0ae4797be10b40ca671dc16fd82f8432b5842b6603033650ee6",
113
+ "language": "Python",
114
+ "lines": 53,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 20653
118
+ },
119
+ {
120
+ "path": "make_universal_variant_ids.py",
121
+ "sha256": "3bcf1e01fb9393db937b56c78d81e2e74d733d0b9121002cf4f7613358e6834a",
122
+ "language": "Python",
123
+ "lines": 94,
124
+ "truncated": false,
125
+ "block": 3,
126
+ "row": 22815
127
+ },
128
+ {
129
+ "path": "manhattan.py",
130
+ "sha256": "8d14a8f07225577c8e7107462a1c44a6863173356992dfefb08ef5ed3edffb8d",
131
+ "language": "Python",
132
+ "lines": 529,
133
+ "truncated": false,
134
+ "block": 3,
135
+ "row": 27370
136
+ },
137
+ {
138
+ "path": "merge_bed_files.py",
139
+ "sha256": "0ee79ec513d9f355441dc2cf63b6de6dfc2818359218e4cd8b2db50f1693b00d",
140
+ "language": "Python",
141
+ "lines": 55,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 20589
145
+ },
146
+ {
147
+ "path": "overCorrect.py",
148
+ "sha256": "ab06c7a3425888bb6b0f1aea44fd4b4ed26cf3eed55b3b18a4f5ec0558e5157c",
149
+ "language": "Python",
150
+ "lines": 34,
151
+ "truncated": false,
152
+ "block": 3,
153
+ "row": 19346
154
+ },
155
+ {
156
+ "path": "plink_utils.py",
157
+ "sha256": "ea96d19e3a7ef534e6b41cd936520245ed1ca3cf739035661e60404b5f4a1655",
158
+ "language": "Python",
159
+ "lines": 85,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 21137
163
+ },
164
+ {
165
+ "path": "plotgwas.py",
166
+ "sha256": "b06921b8873cc487d932711864ee93745bd2f1f675f7ceff0dc4036f58a626f4",
167
+ "language": "Python",
168
+ "lines": 258,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 25735
172
+ },
173
+ {
174
+ "path": "process_metal.py",
175
+ "sha256": "402dedce125fe44b8da2758ba0db95da54ccd8c9e9de6b941105301be130fddf",
176
+ "language": "Python",
177
+ "lines": 33,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 19485
181
+ },
182
+ {
183
+ "path": "pyliftover/__init__.py",
184
+ "sha256": "94e0b1eba58064ee1b3d4119023069e615b646de00cad2fdcca47892d898238f",
185
+ "language": "Python",
186
+ "lines": 33,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 19738
190
+ },
191
+ {
192
+ "path": "pyliftover/chainfile.py",
193
+ "sha256": "bbd42cf0218337d6ede43d5b67202d9fb85b3acb60b418473ea4898fcf92bacd",
194
+ "language": "Python",
195
+ "lines": 224,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 25428
199
+ },
200
+ {
201
+ "path": "pyliftover/intervaltree.py",
202
+ "sha256": "167d885f6db410e7571509fba7e761d522625283fd3ceb30e49f1a29cde907f9",
203
+ "language": "Python",
204
+ "lines": 177,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 23891
208
+ },
209
+ {
210
+ "path": "pyliftover/liftover.py",
211
+ "sha256": "a36d24f32c2cdd2e37b9c9dcd6b87704c0da53b433313c4a5220633fcd48f60d",
212
+ "language": "Python",
213
+ "lines": 94,
214
+ "truncated": false,
215
+ "block": 3,
216
+ "row": 23155
217
+ },
218
+ {
219
+ "path": "qq.py",
220
+ "sha256": "46af9e355a3765421735951fe9fa129b7db4cb3658ee9f620bda5838f0c45887",
221
+ "language": "Python",
222
+ "lines": 386,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 26726
226
+ },
227
+ {
228
+ "path": "sumStats2ref.py",
229
+ "sha256": "a199999a543d77c6e2439b6ef277eb21015e045e1584f591c1a75309251516da",
230
+ "language": "Python",
231
+ "lines": 377,
232
+ "truncated": false,
233
+ "block": 3,
234
+ "row": 26407
235
+ },
236
+ {
237
+ "path": "summary_stats_Utils.py",
238
+ "sha256": "9fc0c7140d87c2b212d3e7c9fa4db4aca8b1ccb6da60ff7870527968c52aaa18",
239
+ "language": "Python",
240
+ "lines": 764,
241
+ "truncated": false,
242
+ "block": 3,
243
+ "row": 27556
244
+ },
245
+ {
246
+ "path": "sumstats.py",
247
+ "sha256": "b90f68f59ae9e704908fec7ff2e8a87cae284d08ee27156bc9e3cf33a01b5df3",
248
+ "language": "Python",
249
+ "lines": 2299,
250
+ "truncated": false,
251
+ "block": 4,
252
+ "row": 104
253
+ },
254
+ {
255
+ "path": "sumstats2mat.py",
256
+ "sha256": "3d3ba5eae0e3a25dd306f0b90c8cd1d607ae034e3a6e577a83e92dce3fe1654e",
257
+ "language": "Python",
258
+ "lines": 180,
259
+ "truncated": false,
260
+ "block": 3,
261
+ "row": 25211
262
+ },
263
+ {
264
+ "path": "sumstats_ldsc_helper.py",
265
+ "sha256": "3bce2b57f6beb94f85343e36a9e7a4cbb3826e19430dcb36cc27e4201f13252e",
266
+ "language": "Python",
267
+ "lines": 80,
268
+ "truncated": false,
269
+ "block": 3,
270
+ "row": 22550
271
+ },
272
+ {
273
+ "path": "sumstats_utils.py",
274
+ "sha256": "b97109461e8fc587e376c629ea7b7217e4ef289e1a8636db296df639a2adc810",
275
+ "language": "Python",
276
+ "lines": 301,
277
+ "truncated": false,
278
+ "block": 3,
279
+ "row": 25537
280
+ },
281
+ {
282
+ "path": "tests/test_consistent.py",
283
+ "sha256": "a8fae64a9d847004915a978972686e26b5ae2efa7767baebeebe93ff664a4a15",
284
+ "language": "Python",
285
+ "lines": 31,
286
+ "truncated": false,
287
+ "block": 3,
288
+ "row": 19515
289
+ },
290
+ {
291
+ "path": "tests/test_duplicated.py",
292
+ "sha256": "7c4df5fee44f3de416606e8d04451fc66aa2e627aa3cb8bc63fa81abf5d73746",
293
+ "language": "Python",
294
+ "lines": 19,
295
+ "truncated": false,
296
+ "block": 3,
297
+ "row": 18797
298
+ },
299
+ {
300
+ "path": "version.py",
301
+ "sha256": "0aa98e8276f959a8e6befc97489405dcf1a37fcf52060ea37f5d107c8593d577",
302
+ "language": "Python",
303
+ "lines": 1,
304
+ "truncated": false,
305
+ "block": 3,
306
+ "row": 17357
307
+ }
308
+ ]
309
+ }
manifests/ff/zenodo__19471544.json ADDED
@@ -0,0 +1,543 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "format": "oscr-script-manifest/1",
3
+ "repository": "zenodo:19471544",
4
+ "url": "10.5281/ZENODO.19471544",
5
+ "host": "zenodo.org",
6
+ "commit": "",
7
+ "license": "BSD-3-Clause",
8
+ "license_confirmed_by": "license file LICENSE",
9
+ "redistribution": "yes",
10
+ "files": [
11
+ {
12
+ "path": "01_convert_to_bids.sh",
13
+ "sha256": "8435de9a956a37ef0e7e6d9a78456f11df9de0e34f9fa8c80358767e34d8e1e6",
14
+ "language": "Shell",
15
+ "lines": 291,
16
+ "truncated": false,
17
+ "block": 4,
18
+ "row": 2241
19
+ },
20
+ {
21
+ "path": "02_run_freesurfer.sh",
22
+ "sha256": "508fba9520eb20a64874ad73fa4b4e417646227608fb61d5e771e8d9634023a8",
23
+ "language": "Shell",
24
+ "lines": 40,
25
+ "truncated": false,
26
+ "block": 4,
27
+ "row": 1785
28
+ },
29
+ {
30
+ "path": "03_run_sswarper.sh",
31
+ "sha256": "92a83075a0fef1d9772e7ea1dfda2132d0627508707f5a111d34ddff36cc9f24",
32
+ "language": "Shell",
33
+ "lines": 31,
34
+ "truncated": false,
35
+ "block": 4,
36
+ "row": 1724
37
+ },
38
+ {
39
+ "path": "04_run_suma.sh",
40
+ "sha256": "3376a2587aafcbf1b7f691a904af6e6c5c700eb62faf5e01edf463e9e35fdb25",
41
+ "language": "Shell",
42
+ "lines": 25,
43
+ "truncated": false,
44
+ "block": 4,
45
+ "row": 1654
46
+ },
47
+ {
48
+ "path": "05_plot_fd_alltasks.py",
49
+ "sha256": "294fb21be1a2f096bb887cc65168dd6bbf945fd31e6ba2011d5cef21cdee7c2b",
50
+ "language": "Python",
51
+ "lines": 188,
52
+ "truncated": false,
53
+ "block": 3,
54
+ "row": 24596
55
+ },
56
+ {
57
+ "path": "99_master_script.sh",
58
+ "sha256": "89679250bac0577d7eea4af6beadfa4b4eb355e8cd3d65c70b729e10680ca613",
59
+ "language": "Shell",
60
+ "lines": 22,
61
+ "truncated": false,
62
+ "block": 4,
63
+ "row": 1739
64
+ },
65
+ {
66
+ "path": "LICENSE",
67
+ "sha256": "2b8fec9637e43df58d093bf7de55fb35639054369a96f1cbeadc2efd348811d7",
68
+ "language": "License",
69
+ "lines": 28,
70
+ "truncated": false,
71
+ "block": 3,
72
+ "row": 8108
73
+ },
74
+ {
75
+ "path": "README.md",
76
+ "sha256": "276daeb2152903f9e1e5788f6fe3843acd338a5705f040ebd926aadc63f17908",
77
+ "language": "Text",
78
+ "lines": 45,
79
+ "truncated": false,
80
+ "block": 4,
81
+ "row": 2432
82
+ },
83
+ {
84
+ "path": "add_intendedfor_field.py",
85
+ "sha256": "8d92c927fab4e43a8c371855a98a2f1283a1cb63b7adbce6f273bfe041c6e12f",
86
+ "language": "Python",
87
+ "lines": 89,
88
+ "truncated": false,
89
+ "block": 3,
90
+ "row": 22013
91
+ },
92
+ {
93
+ "path": "backtothefuture/01_preprocess_btf.sh",
94
+ "sha256": "3d0eae4ab662cef405265789a91eb2474d587dfea9c38348850ba1d4a5cd2918",
95
+ "language": "Shell",
96
+ "lines": 169,
97
+ "truncated": false,
98
+ "block": 4,
99
+ "row": 2228
100
+ },
101
+ {
102
+ "path": "backtothefuture/02_plot_fd.py",
103
+ "sha256": "8dd71dda24e830db3b362296b267d38a4ce0aec1197c7d11cf2fa5df59c1749f",
104
+ "language": "Python",
105
+ "lines": 146,
106
+ "truncated": false,
107
+ "block": 3,
108
+ "row": 23434
109
+ },
110
+ {
111
+ "path": "backtothefuture/03_extract_motion.py",
112
+ "sha256": "9e07f7fa0f77ac9af12da15cdf7f2d79f96b99869d930af16dcd15c5905bf5ca",
113
+ "language": "Python",
114
+ "lines": 87,
115
+ "truncated": false,
116
+ "block": 3,
117
+ "row": 22158
118
+ },
119
+ {
120
+ "path": "backtothefuture/04_calc_tsnr.sh",
121
+ "sha256": "58b40597a27ab593cba9c0cc1b0d8899c13e64ccb0002727b0cc6bdc6908c941",
122
+ "language": "Shell",
123
+ "lines": 71,
124
+ "truncated": false,
125
+ "block": 4,
126
+ "row": 2063
127
+ },
128
+ {
129
+ "path": "backtothefuture/05_calc_grouptsnr.sh",
130
+ "sha256": "4e4fe5fc66326e984b4be5a5ad9aa778f402a2c310049b68e5b0080e5aa31b94",
131
+ "language": "Shell",
132
+ "lines": 31,
133
+ "truncated": false,
134
+ "block": 4,
135
+ "row": 1742
136
+ },
137
+ {
138
+ "path": "backtothefuture/06_plot_tsnr.py",
139
+ "sha256": "f0030bb328d40d557c86866453e11c38729167d9c34b1d6dffb59b16c90fdee1",
140
+ "language": "Python",
141
+ "lines": 59,
142
+ "truncated": false,
143
+ "block": 3,
144
+ "row": 20154
145
+ },
146
+ {
147
+ "path": "backtothefuture/07_run_isc.sh",
148
+ "sha256": "42c97e69b789beab00bc6c0b67e4bd4bb8503e905be29969e055d5d1e8e5716f",
149
+ "language": "Shell",
150
+ "lines": 86,
151
+ "truncated": false,
152
+ "block": 4,
153
+ "row": 2062
154
+ },
155
+ {
156
+ "path": "backtothefuture/08_plot_isc.py",
157
+ "sha256": "4f8162080c39a276a677992c3dee32d855af2ebf80b7fdca058cbc59a3f36e73",
158
+ "language": "Python",
159
+ "lines": 122,
160
+ "truncated": false,
161
+ "block": 3,
162
+ "row": 22515
163
+ },
164
+ {
165
+ "path": "backtothefuture/09_extract_cals.py",
166
+ "sha256": "a5f67f5158fbc447b61e4bf4e65af954e87a5d0487d270dc6a34454290f140ad",
167
+ "language": "Python",
168
+ "lines": 100,
169
+ "truncated": false,
170
+ "block": 3,
171
+ "row": 21591
172
+ },
173
+ {
174
+ "path": "cognitron_tobidsfolder.py",
175
+ "sha256": "a2147c8f7869fad777bdeb1d8ad62dfcc207f612c834e51f39afba353ccd2bf0",
176
+ "language": "Python",
177
+ "lines": 45,
178
+ "truncated": false,
179
+ "block": 3,
180
+ "row": 19764
181
+ },
182
+ {
183
+ "path": "heuristic_sess01.py",
184
+ "sha256": "ef8da9a956603b49001d7643fd8d68231d54d1f82fa7ae329b77ccb9b7dfa5e2",
185
+ "language": "Python",
186
+ "lines": 184,
187
+ "truncated": false,
188
+ "block": 3,
189
+ "row": 25179
190
+ },
191
+ {
192
+ "path": "heuristic_sess02.py",
193
+ "sha256": "b4e3a4354d89ca3043f844cb14557e63edbc656c795e9eb47de89be5d5c7e605",
194
+ "language": "Python",
195
+ "lines": 189,
196
+ "truncated": false,
197
+ "block": 3,
198
+ "row": 25196
199
+ },
200
+ {
201
+ "path": "pulselog2sourcedata.py",
202
+ "sha256": "cb34834d4d35fed3fd79a65ccba9c9ab46180419d7752939f086b9fe9d1527db",
203
+ "language": "Python",
204
+ "lines": 114,
205
+ "truncated": false,
206
+ "block": 3,
207
+ "row": 23659
208
+ },
209
+ {
210
+ "path": "retinotopy/01_preprocess_retinotopy.sh",
211
+ "sha256": "b1a8339962e1fff96655231aa34b1caf99d3873014e1bc51e0330a8d7e2605cd",
212
+ "language": "Shell",
213
+ "lines": 93,
214
+ "truncated": false,
215
+ "block": 4,
216
+ "row": 2162
217
+ },
218
+ {
219
+ "path": "retinotopy/02_get_mincosts.py",
220
+ "sha256": "f8158743a70afe7553411a6279b20174f4c48f6cafea5c8c079c2ad1e8538dfc",
221
+ "language": "Python",
222
+ "lines": 40,
223
+ "truncated": false,
224
+ "block": 3,
225
+ "row": 19217
226
+ },
227
+ {
228
+ "path": "retinotopy/03_reprocess_retinotopy.sh",
229
+ "sha256": "8bcaec780ef9183423c9e79216b5f9c97f06509930e6d008431b42a49ac7f29e",
230
+ "language": "Shell",
231
+ "lines": 88,
232
+ "truncated": false,
233
+ "block": 4,
234
+ "row": 2150
235
+ },
236
+ {
237
+ "path": "retinotopy/04_plot_fd.py",
238
+ "sha256": "7f0175ae17d3bdc6c0d0e8d27da532690275be0009fd7210d79fe0039b0f416c",
239
+ "language": "Python",
240
+ "lines": 107,
241
+ "truncated": false,
242
+ "block": 3,
243
+ "row": 22460
244
+ },
245
+ {
246
+ "path": "retinotopy/05_extract_motion.py",
247
+ "sha256": "97a7ce36342a12d2bf54e5bcd5d9dd8543cc3b3a00127858c5eaaef277ebbe7f",
248
+ "language": "Python",
249
+ "lines": 104,
250
+ "truncated": false,
251
+ "block": 3,
252
+ "row": 22590
253
+ },
254
+ {
255
+ "path": "retinotopy/06_run_surfprojection.sh",
256
+ "sha256": "86155966379dbc8d8cc41f064bb63c1ffb8c3f9a7789996aab0b845cc4b47a41",
257
+ "language": "Shell",
258
+ "lines": 9,
259
+ "truncated": false,
260
+ "block": 4,
261
+ "row": 1427
262
+ },
263
+ {
264
+ "path": "retinotopy/07_run_fitprf.sh",
265
+ "sha256": "f882d5301f787fe3a433e6f2d2a2959f9381fcaf6473dca99cdc4b056b49dc51",
266
+ "language": "Shell",
267
+ "lines": 28,
268
+ "truncated": false,
269
+ "block": 4,
270
+ "row": 1759
271
+ },
272
+ {
273
+ "path": "retinotopy/08_run_nativetotemplate.sh",
274
+ "sha256": "b2b79c990aac005ff0083b6994367fb7c85312208a7545dcac23e841d19f6d8f",
275
+ "language": "Shell",
276
+ "lines": 10,
277
+ "truncated": false,
278
+ "block": 4,
279
+ "row": 1437
280
+ },
281
+ {
282
+ "path": "retinotopy/09_run_generateavgmap.sh",
283
+ "sha256": "a69893f97748a6b2ec0c311bbdd18dee15e816fd7a6ea40ed7496a73f2e61f18",
284
+ "language": "Shell",
285
+ "lines": 10,
286
+ "truncated": false,
287
+ "block": 4,
288
+ "row": 1435
289
+ },
290
+ {
291
+ "path": "retinotopy/FS_SurfaceProjection_MGHtoMAT.m",
292
+ "sha256": "b3a58cb052c43c0a1dfa16c1253a29f329c84ebd75d71551bf9df47e1cac4bd0",
293
+ "language": "MATLAB",
294
+ "lines": 135,
295
+ "truncated": false,
296
+ "block": 3,
297
+ "row": 14445
298
+ },
299
+ {
300
+ "path": "retinotopy/SupportingScripts/CalculateVDM.m",
301
+ "sha256": "96bfe73023c41476e228d2e0e05102253d1ed1582593f23ac90f946b1d92bdb2",
302
+ "language": "MATLAB",
303
+ "lines": 33,
304
+ "truncated": false,
305
+ "block": 3,
306
+ "row": 13048
307
+ },
308
+ {
309
+ "path": "retinotopy/SupportingScripts/Combine_BilateralSrf.m",
310
+ "sha256": "b77afccab9888554460aafcd3627d8d35b10ac0b1d57896e1ebc71bc38dab884",
311
+ "language": "MATLAB",
312
+ "lines": 68,
313
+ "truncated": false,
314
+ "block": 3,
315
+ "row": 12486
316
+ },
317
+ {
318
+ "path": "retinotopy/SupportingScripts/PlotpRFParams_Fit.m",
319
+ "sha256": "88ca646e9d921156f27c75584d2344704fa0ae3000081f7ab0bccc1607aa1dc5",
320
+ "language": "MATLAB",
321
+ "lines": 84,
322
+ "truncated": false,
323
+ "block": 3,
324
+ "row": 14033
325
+ },
326
+ {
327
+ "path": "retinotopy/SupportingScripts/Read_JsonHeader.m",
328
+ "sha256": "718ca3f5a2e1526c1779edd716da8c8cf308c9bc109bde67aa8f920f67c22105",
329
+ "language": "MATLAB",
330
+ "lines": 55,
331
+ "truncated": false,
332
+ "block": 3,
333
+ "row": 11140
334
+ },
335
+ {
336
+ "path": "retinotopy/SupportingScripts/UnderstandStimuluspRF.m",
337
+ "sha256": "0f1377d8ac5c4e6d074f64cf4f18bc3b99d08efccc31ee931e4d0eea5bece668",
338
+ "language": "MATLAB",
339
+ "lines": 48,
340
+ "truncated": false,
341
+ "block": 3,
342
+ "row": 12039
343
+ },
344
+ {
345
+ "path": "retinotopy/SupportingScripts/Visual_Angle.m",
346
+ "sha256": "ee7542c233864762e84c7e73b97a0127ef0c45c1d93b13b4361dd6656b7fe850",
347
+ "language": "MATLAB",
348
+ "lines": 16,
349
+ "truncated": false,
350
+ "block": 3,
351
+ "row": 8827
352
+ },
353
+ {
354
+ "path": "retinotopy/SupportingScripts/batch_job.m",
355
+ "sha256": "9e61629101b889b23e84374a8017f0d03974f628ebdfb92a9dfd64a46eafeafe",
356
+ "language": "MATLAB",
357
+ "lines": 76,
358
+ "truncated": false,
359
+ "block": 3,
360
+ "row": 14890
361
+ },
362
+ {
363
+ "path": "retinotopy/SupportingScripts/batch_job_3T_dual.m",
364
+ "sha256": "5063fa1b3b0bd9f444b618af36c96a568d4c9fb6acb6d90e6d6b80a5f1abff17",
365
+ "language": "MATLAB",
366
+ "lines": 69,
367
+ "truncated": false,
368
+ "block": 3,
369
+ "row": 14554
370
+ },
371
+ {
372
+ "path": "retinotopy/SupportingScripts/batch_job_3T_single.m",
373
+ "sha256": "9c95908f4125492b85ff57847578bcfbf8c5cdfbb8b3387793a704139a8a219c",
374
+ "language": "MATLAB",
375
+ "lines": 65,
376
+ "truncated": false,
377
+ "block": 3,
378
+ "row": 14180
379
+ },
380
+ {
381
+ "path": "retinotopy/SupportingScripts/fit_prf_V7.m",
382
+ "sha256": "fdc98838a85cf407f60f96fcd1756c5ea52a0b0811a29cc07e5e551599540c0b",
383
+ "language": "MATLAB",
384
+ "lines": 52,
385
+ "truncated": false,
386
+ "block": 3,
387
+ "row": 12713
388
+ },
389
+ {
390
+ "path": "retinotopy/SupportingScripts/make_Ascii.m",
391
+ "sha256": "e03eb1111fda31897eb8522e4e403e5059b2ec05abea647100fadc601f2dc602",
392
+ "language": "MATLAB",
393
+ "lines": 29,
394
+ "truncated": false,
395
+ "block": 3,
396
+ "row": 12946
397
+ },
398
+ {
399
+ "path": "retinotopy/SupportingScripts/project2surf_V7.m",
400
+ "sha256": "2ba9da755c98548a3514000d7dd3f215341a88de890acc42310ba5fcbeffcd25",
401
+ "language": "MATLAB",
402
+ "lines": 30,
403
+ "truncated": false,
404
+ "block": 3,
405
+ "row": 9344
406
+ },
407
+ {
408
+ "path": "retinotopy/SupportingScripts/spm_preprocessing.m",
409
+ "sha256": "b56da9ae1a08d6ea955c0d3fb464d1a6ee32576ab475eb9b31fa9aa1adae5b78",
410
+ "language": "MATLAB",
411
+ "lines": 181,
412
+ "truncated": false,
413
+ "block": 3,
414
+ "row": 15721
415
+ },
416
+ {
417
+ "path": "retinotopy/generate_avgmap.m",
418
+ "sha256": "32706606504d00e1ba18c8098e9ed827d3f653b62a9d9f06ea8c416dab27d399",
419
+ "language": "MATLAB",
420
+ "lines": 76,
421
+ "truncated": false,
422
+ "block": 3,
423
+ "row": 12661
424
+ },
425
+ {
426
+ "path": "retinotopy/map_to_fsaverage.m",
427
+ "sha256": "0ba37f49aab63e8bfb365dbdfbc27ca6466aca3e5fe415aaf0da9b4aeb97c6b3",
428
+ "language": "MATLAB",
429
+ "lines": 73,
430
+ "truncated": false,
431
+ "block": 3,
432
+ "row": 12565
433
+ },
434
+ {
435
+ "path": "retinotopy/run_pRF_V7.m",
436
+ "sha256": "b18f8c8b285cbbca04f05a8b3c7c95edea2fa19c30727e7a258ef92b612f677b",
437
+ "language": "MATLAB",
438
+ "lines": 102,
439
+ "truncated": false,
440
+ "block": 3,
441
+ "row": 13553
442
+ },
443
+ {
444
+ "path": "retinotopy_behaviour.py",
445
+ "sha256": "21634f8af8f4d963e8b21b48a371d571ad45157fc2a0cb98ac40266d8dddf462",
446
+ "language": "Python",
447
+ "lines": 65,
448
+ "truncated": false,
449
+ "block": 3,
450
+ "row": 20826
451
+ },
452
+ {
453
+ "path": "somatotopy/01_preprocess_somatotopy.sh",
454
+ "sha256": "b8e62860b6055fe155f692a32d4bc5972f1763edc03304485340a446a3322876",
455
+ "language": "Shell",
456
+ "lines": 132,
457
+ "truncated": false,
458
+ "block": 4,
459
+ "row": 2203
460
+ },
461
+ {
462
+ "path": "somatotopy/02_plot_fd.py",
463
+ "sha256": "bd25f4b8fe3336f7b24e33f015619d8ac4d1b5b5a47a154030aff0eff9b58b4e",
464
+ "language": "Python",
465
+ "lines": 189,
466
+ "truncated": false,
467
+ "block": 3,
468
+ "row": 24251
469
+ },
470
+ {
471
+ "path": "somatotopy/03_extract_motion.py",
472
+ "sha256": "dbc073db78b417953621e34c8d85143133d7f3415da66c83ef2ec55065ad3a4c",
473
+ "language": "Python",
474
+ "lines": 123,
475
+ "truncated": false,
476
+ "block": 3,
477
+ "row": 23164
478
+ },
479
+ {
480
+ "path": "somatotopy/04_group_ttest.sh",
481
+ "sha256": "e6d7f0031893a55a434c43c6bbb9059f2fdc8503f9a2db74782e4c3dbe0e406a",
482
+ "language": "Shell",
483
+ "lines": 135,
484
+ "truncated": false,
485
+ "block": 4,
486
+ "row": 2165
487
+ },
488
+ {
489
+ "path": "somatotopy/plot_tsnr.py",
490
+ "sha256": "8c726e04471ab137e6e8fdd50e321ce804eaa268a3d3102f224b76d27eb8d4d7",
491
+ "language": "Python",
492
+ "lines": 127,
493
+ "truncated": false,
494
+ "block": 3,
495
+ "row": 22736
496
+ },
497
+ {
498
+ "path": "tonotopy/01_preprocess_tonotopy.sh",
499
+ "sha256": "fe002037e2ae4bc1e79ff81d424fe4a15fb3405e9563044c6eea80547eaaee62",
500
+ "language": "Shell",
501
+ "lines": 93,
502
+ "truncated": false,
503
+ "block": 4,
504
+ "row": 2154
505
+ },
506
+ {
507
+ "path": "tonotopy/02_plot_fd.py",
508
+ "sha256": "4d9da8a234afed444be227ae7df30891384d4f2719e3563d430f2cca9f1731e1",
509
+ "language": "Python",
510
+ "lines": 107,
511
+ "truncated": false,
512
+ "block": 3,
513
+ "row": 22345
514
+ },
515
+ {
516
+ "path": "tonotopy/03_extract_motion.py",
517
+ "sha256": "424ac2777012dcb41b943135501e02ed1ad16f87135c23aab8dd4cbdf5f173cc",
518
+ "language": "Python",
519
+ "lines": 103,
520
+ "truncated": false,
521
+ "block": 3,
522
+ "row": 22541
523
+ },
524
+ {
525
+ "path": "tonotopy/04_get_mincosts.py",
526
+ "sha256": "df7852dbeeabe9a759b7f46d3652b93e61215d94a54347c3b40e20aca173016d",
527
+ "language": "Python",
528
+ "lines": 40,
529
+ "truncated": false,
530
+ "block": 3,
531
+ "row": 19208
532
+ },
533
+ {
534
+ "path": "tonotopy_behaviour.py",
535
+ "sha256": "44396eb1a646de038c733567c14648a184351f802bd8b924344b9c3762900262",
536
+ "language": "Python",
537
+ "lines": 136,
538
+ "truncated": false,
539
+ "block": 3,
540
+ "row": 22800
541
+ }
542
+ ]
543
+ }