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Datasets:
yashvir
/
seq2state-data

Tasks:
Tabular Regression
Tabular Classification
Modalities:
Text
Tags:
genomics
crispr
enhancer-gene
perturb-seq
License:
Dataset card Data Studio Files
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  1. data/processed/.gitkeep +1 -0
  2. data/processed/s2t/fulco2019_k562/features/sequence_to_function_oracle_features.alphagenome_counterfactual_fulco2019.parquet.metadata.yaml +113 -0
  3. data/processed/s2t/fulco2019_k562/qc_summary.yaml +8 -0
  4. data/processed/s2t/gasperini_gse120861/abc_annotation_qc.yaml +9 -0
  5. data/processed/s2t/gasperini_gse120861/ccre_annotation_qc.yaml +14 -0
  6. data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_all_positive_pairs.csv +0 -0
  7. data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_all_positive_pairs.parquet.metadata.yaml +19 -0
  8. data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top100_pairs.csv +0 -0
  9. data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top100_pairs.parquet.metadata.yaml +19 -0
  10. data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top250_pairs.csv +0 -0
  11. data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top250_pairs.parquet.metadata.yaml +19 -0
  12. data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top50_pairs.csv +0 -0
  13. data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top50_pairs.parquet.metadata.yaml +19 -0
  14. data/processed/s2t/gasperini_gse120861/features/external_e2g/encode_re2g_k562_extended_full_feature_metadata.csv +47 -0
  15. data/processed/s2t/gasperini_gse120861/features/external_e2g/encode_re2g_k562_extended_full_features.parquet +3 -0
  16. data/processed/s2t/gasperini_gse120861/features/external_e2g/external_e2g_feature_build_summary.csv +2 -0
  17. data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_feature_metadata.csv +18 -0
  18. data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet +3 -0
  19. data/processed/s2t/gasperini_gse120861/features/k562_counterfactual_proxy_features.parquet.metadata.yaml +23 -0
  20. data/processed/s2t/gasperini_gse120861/features/k562_counterfactual_proxy_features_v2.metadata.yaml +25 -0
  21. data/processed/s2t/gasperini_gse120861/features/k562_counterfactual_proxy_features_v2.parquet.feature_families.csv +274 -0
  22. data/processed/s2t/gasperini_gse120861/features/k562_counterfactual_proxy_features_v2.parquet.metadata.yaml +24 -0
  23. data/processed/s2t/gasperini_gse120861/features/k562_expression_feature_metadata.yaml +20 -0
  24. data/processed/s2t/gasperini_gse120861/features/k562_fantom5_cage_feature_metadata.yaml +70 -0
  25. data/processed/s2t/gasperini_gse120861/features/k562_observed_contact_feature_metadata.csv +9 -0
  26. data/processed/s2t/gasperini_gse120861/features/k562_observed_contact_recomputed_abc_metadata.csv +65 -0
  27. data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_metadata.csv +18 -0
  28. data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet +3 -0
  29. data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_recomputed_abc_metadata.csv +65 -0
  30. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_pilot.parquet.metadata.yaml +18 -0
  31. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_region_complete_all_positive.parquet.metadata.yaml +38 -0
  32. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_region_complete_top100.parquet.metadata.yaml +18 -0
  33. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_region_complete_top250.parquet.metadata.yaml +18 -0
  34. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_region_complete_top50.parquet.metadata.yaml +18 -0
  35. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_smoke.parquet +3 -0
  36. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_smoke.parquet.metadata.yaml +18 -0
  37. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_pilot.parquet.metadata.yaml +15 -0
  38. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_region_complete_top50.parquet.metadata.yaml +18 -0
  39. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_smoke.parquet.metadata.yaml +15 -0
  40. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.open_model_counterfactual_pilot.parquet.metadata.yaml +11 -0
  41. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_pilot_pairs.csv +51 -0
  42. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_pilot_pairs.metadata.yaml +17 -0
  43. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_requests.alphagenome.jsonl +50 -0
  44. data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_requests.alphagenome.jsonl.metadata.yaml +14 -0
  45. data/processed/s2t/gasperini_gse120861/qc_summary.yaml +12 -0
  46. data/processed/s2t/gm12878_heldout/qc_summary.yaml +8 -0
  47. data/processed/s2t/hct116_heldout/qc_summary.yaml +8 -0
  48. data/processed/t2s/vcc_2025/perturbation_response_stats_qc.yaml +10 -0
  49. data/processed/t2s/vcc_2025/perturbation_signature_qc.yaml +10 -0
  50. data/processed/t2s/vcc_2025/smoke_perturbation_signature_qc.yaml +10 -0
data/processed/.gitkeep ADDED
@@ -0,0 +1 @@
 
 
1
+
data/processed/s2t/fulco2019_k562/features/sequence_to_function_oracle_features.alphagenome_counterfactual_fulco2019.parquet.metadata.yaml ADDED
@@ -0,0 +1,113 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: AlphaGenome API K562 enhancer-masking counterfactual
2
+ output: data/processed/s2t/fulco2019_k562/features/sequence_to_function_oracle_features.alphagenome_counterfactual_fulco2019.parquet
3
+ pairs: data/processed/s2t/fulco2019_k562/alphagenome_panel_pairs.parquet
4
+ lifted_anchors: data/processed/s2t/fulco2019_k562/alphagenome_panel_anchors.parquet
5
+ feature_set: alphagenome_k562_counterfactual_fulco2019
6
+ ontology_term: EFO:0002067
7
+ mask_base: N
8
+ region_window_bp: 2000
9
+ promoter_window_bp: 2000
10
+ flank_bp: 8192
11
+ n_completed_pairs_loaded: 0
12
+ n_input_pairs: 263
13
+ n_scored_pairs: 244
14
+ n_feature_rows: 8784
15
+ n_failures: 19
16
+ failures:
17
+ - oracle_request_id: s2f_scale_00014_fulco2019|chr19:12671911-12672491_C19orf43
18
+ region_id: fulco2019|chr19:12671911-12672491
19
+ gene_id: C19orf43
20
+ error: ValueError('Pair span 12688586 bp exceeds maximum supported AlphaGenome window
21
+ 1048576 bp')
22
+ - oracle_request_id: s2f_scale_00024_fulco2019|chr19:12777511-12778031_C19orf43
23
+ region_id: fulco2019|chr19:12777511-12778031
24
+ gene_id: C19orf43
25
+ error: ValueError('Pair span 12794156 bp exceeds maximum supported AlphaGenome window
26
+ 1048576 bp')
27
+ - oracle_request_id: s2f_scale_00035_fulco2019|chr19:12779131-12779731_C19orf43
28
+ region_id: fulco2019|chr19:12779131-12779731
29
+ gene_id: C19orf43
30
+ error: ValueError('Pair span 12795816 bp exceeds maximum supported AlphaGenome window
31
+ 1048576 bp')
32
+ - oracle_request_id: s2f_scale_00047_fulco2019|chr19:12782291-12783171_C19orf43
33
+ region_id: fulco2019|chr19:12782291-12783171
34
+ gene_id: C19orf43
35
+ error: ValueError('Pair span 12799116 bp exceeds maximum supported AlphaGenome window
36
+ 1048576 bp')
37
+ - oracle_request_id: s2f_scale_00058_fulco2019|chr19:12784451-12784971_C19orf43
38
+ region_id: fulco2019|chr19:12784451-12784971
39
+ gene_id: C19orf43
40
+ error: ValueError('Pair span 12801096 bp exceeds maximum supported AlphaGenome window
41
+ 1048576 bp')
42
+ - oracle_request_id: s2f_scale_00068_fulco2019|chr19:12789831-12790351_C19orf43
43
+ region_id: fulco2019|chr19:12789831-12790351
44
+ gene_id: C19orf43
45
+ error: ValueError('Pair span 12806476 bp exceeds maximum supported AlphaGenome window
46
+ 1048576 bp')
47
+ - oracle_request_id: s2f_scale_00079_fulco2019|chr19:12825131-12825931_C19orf43
48
+ region_id: fulco2019|chr19:12825131-12825931
49
+ gene_id: C19orf43
50
+ error: ValueError('Pair span 12841916 bp exceeds maximum supported AlphaGenome window
51
+ 1048576 bp')
52
+ - oracle_request_id: s2f_scale_00090_fulco2019|chr19:12847511-12848011_C19orf43
53
+ region_id: fulco2019|chr19:12847511-12848011
54
+ gene_id: C19orf43
55
+ error: ValueError('Pair span 12864146 bp exceeds maximum supported AlphaGenome window
56
+ 1048576 bp')
57
+ - oracle_request_id: s2f_scale_00101_fulco2019|chr19:12867151-12867931_C19orf43
58
+ region_id: fulco2019|chr19:12867151-12867931
59
+ gene_id: C19orf43
60
+ error: ValueError('Pair span 12883926 bp exceeds maximum supported AlphaGenome window
61
+ 1048576 bp')
62
+ - oracle_request_id: s2f_scale_00112_fulco2019|chr19:12882571-12883071_C19orf43
63
+ region_id: fulco2019|chr19:12882571-12883071
64
+ gene_id: C19orf43
65
+ error: ValueError('Pair span 12899206 bp exceeds maximum supported AlphaGenome window
66
+ 1048576 bp')
67
+ - oracle_request_id: s2f_scale_00121_fulco2019|chr19:12883611-12884131_C19orf43
68
+ region_id: fulco2019|chr19:12883611-12884131
69
+ gene_id: C19orf43
70
+ error: ValueError('Pair span 12900256 bp exceeds maximum supported AlphaGenome window
71
+ 1048576 bp')
72
+ - oracle_request_id: s2f_scale_00131_fulco2019|chr19:12885011-12885511_C19orf43
73
+ region_id: fulco2019|chr19:12885011-12885511
74
+ gene_id: C19orf43
75
+ error: ValueError('Pair span 12901646 bp exceeds maximum supported AlphaGenome window
76
+ 1048576 bp')
77
+ - oracle_request_id: s2f_scale_00140_fulco2019|chr19:12888891-12889391_C19orf43
78
+ region_id: fulco2019|chr19:12888891-12889391
79
+ gene_id: C19orf43
80
+ error: ValueError('Pair span 12905526 bp exceeds maximum supported AlphaGenome window
81
+ 1048576 bp')
82
+ - oracle_request_id: s2f_scale_00149_fulco2019|chr19:13104331-13104911_C19orf43
83
+ region_id: fulco2019|chr19:13104331-13104911
84
+ gene_id: C19orf43
85
+ error: ValueError('Pair span 13121006 bp exceeds maximum supported AlphaGenome window
86
+ 1048576 bp')
87
+ - oracle_request_id: s2f_scale_00204_fulco2019|chr3:129245622-129246162_SEC61A1
88
+ region_id: fulco2019|chr3:129245622-129246162
89
+ gene_id: SEC61A1
90
+ error: ValueError('Pair span 1210636 bp exceeds maximum supported AlphaGenome window
91
+ 1048576 bp')
92
+ - oracle_request_id: s2f_scale_00209_fulco2019|chr3:129305622-129306122_SEC61A1
93
+ region_id: fulco2019|chr3:129305622-129306122
94
+ gene_id: SEC61A1
95
+ error: ValueError('Pair span 1270616 bp exceeds maximum supported AlphaGenome window
96
+ 1048576 bp')
97
+ - oracle_request_id: s2f_scale_00215_fulco2019|chr8:129581780-129582461_MYC
98
+ region_id: fulco2019|chr8:129581780-129582461
99
+ gene_id: MYC
100
+ error: ValueError('Pair span 1863071 bp exceeds maximum supported AlphaGenome window
101
+ 1048576 bp')
102
+ - oracle_request_id: s2f_scale_00216_fulco2019|chr8:129689360-129689694_MYC
103
+ region_id: fulco2019|chr8:129689360-129689694
104
+ gene_id: MYC
105
+ error: ValueError('Pair span 1970478 bp exceeds maximum supported AlphaGenome window
106
+ 1048576 bp')
107
+ - oracle_request_id: s2f_scale_00217_fulco2019|chr8:129692458-129693217_MYC
108
+ region_id: fulco2019|chr8:129692458-129693217
109
+ gene_id: MYC
110
+ error: ValueError('Pair span 1973788 bp exceeds maximum supported AlphaGenome window
111
+ 1048576 bp')
112
+ terms_ok_for_training: false
113
+ api_key_stored: false
data/processed/s2t/fulco2019_k562/qc_summary.yaml ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ source_dataset: fulco2019_k562
2
+ cell_context: K562
3
+ assembly: hg38
4
+ n_regions: 685
5
+ n_candidate_pairs: 3501
6
+ n_labeled_pairs: 3501
7
+ n_positive_pairs: 52
8
+ prevalence: 0.014852899171665239
data/processed/s2t/gasperini_gse120861/abc_annotation_qc.yaml ADDED
@@ -0,0 +1,9 @@
 
 
 
 
 
 
 
 
 
 
1
+ candidate_pairs: 138057
2
+ pairs_with_abc_score: 8140
3
+ max_abc_score: 0.415391
4
+ mean_nonzero_abc_score: 0.03296178968058968
5
+ abc_predictions: data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz
6
+ regions_assembly:
7
+ - hg19
8
+ abc_assembly: hg19
9
+ allow_assembly_mismatch: false
data/processed/s2t/gasperini_gse120861/ccre_annotation_qc.yaml ADDED
@@ -0,0 +1,14 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ regions: 6143
2
+ regions_with_ccre: 5810
3
+ ccre_class_counts:
4
+ dELS: 5252
5
+ pELS: 463
6
+ unannotated: 333
7
+ PLS: 95
8
+ ccre_beds:
9
+ - data/interim/screen_v4_liftover/hg19/GRCh38-cCREs.PLS.hg19.bed
10
+ - data/interim/screen_v4_liftover/hg19/GRCh38-cCREs.ELS.hg19.bed
11
+ regions_assembly:
12
+ - hg19
13
+ ccre_assembly: hg19
14
+ allow_assembly_mismatch: false
data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_all_positive_pairs.csv ADDED
The diff for this file is too large to render. See raw diff
 
data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_all_positive_pairs.parquet.metadata.yaml ADDED
@@ -0,0 +1,19 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: Seq2State Gasperini labeled candidates
2
+ purpose: Region-complete AlphaGenome scale panel for fairer target-gene ranking evaluation
3
+ selection:
4
+ n_positive_regions: 10000
5
+ rule: Select positive regions by positive count, max absolute effect, max distance,
6
+ and min FDR; include all labeled candidate genes for each selected region.
7
+ output: data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_all_positive_pairs.parquet
8
+ csv_output: data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_all_positive_pairs.csv
9
+ summary:
10
+ n_pairs: 5909
11
+ n_regions: 600
12
+ n_genes: 3748
13
+ n_positive: 664
14
+ n_negative: 5245
15
+ prevalence: 0.11237095955322389
16
+ n_non_nearest: 5453
17
+ n_midrange_100_500kb: 2377
18
+ terms_note: Panel contains benchmark coordinates and labels only. Returned model outputs
19
+ must remain no-training oracle features unless explicit terms review allows training.
data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top100_pairs.csv ADDED
The diff for this file is too large to render. See raw diff
 
data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top100_pairs.parquet.metadata.yaml ADDED
@@ -0,0 +1,19 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: Seq2State Gasperini labeled candidates
2
+ purpose: Region-complete AlphaGenome scale panel for fairer target-gene ranking evaluation
3
+ selection:
4
+ n_positive_regions: 100
5
+ rule: Select positive regions by positive count, max absolute effect, max distance,
6
+ and min FDR; include all labeled candidate genes for each selected region.
7
+ output: data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top100_pairs.parquet
8
+ csv_output: data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top100_pairs.csv
9
+ summary:
10
+ n_pairs: 1063
11
+ n_regions: 100
12
+ n_genes: 906
13
+ n_positive: 164
14
+ n_negative: 899
15
+ prevalence: 0.15428033866415805
16
+ n_non_nearest: 980
17
+ n_midrange_100_500kb: 420
18
+ terms_note: Panel contains benchmark coordinates and labels only. Returned model outputs
19
+ must remain no-training oracle features unless explicit terms review allows training.
data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top250_pairs.csv ADDED
The diff for this file is too large to render. See raw diff
 
data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top250_pairs.parquet.metadata.yaml ADDED
@@ -0,0 +1,19 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: Seq2State Gasperini labeled candidates
2
+ purpose: Region-complete AlphaGenome scale panel for fairer target-gene ranking evaluation
3
+ selection:
4
+ n_positive_regions: 250
5
+ rule: Select positive regions by positive count, max absolute effect, max distance,
6
+ and min FDR; include all labeled candidate genes for each selected region.
7
+ output: data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top250_pairs.parquet
8
+ csv_output: data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top250_pairs.csv
9
+ summary:
10
+ n_pairs: 2303
11
+ n_regions: 250
12
+ n_genes: 1893
13
+ n_positive: 314
14
+ n_negative: 1989
15
+ prevalence: 0.13634389926183238
16
+ n_non_nearest: 2105
17
+ n_midrange_100_500kb: 902
18
+ terms_note: Panel contains benchmark coordinates and labels only. Returned model outputs
19
+ must remain no-training oracle features unless explicit terms review allows training.
data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top50_pairs.csv ADDED
The diff for this file is too large to render. See raw diff
 
data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top50_pairs.parquet.metadata.yaml ADDED
@@ -0,0 +1,19 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: Seq2State Gasperini labeled candidates
2
+ purpose: Region-complete AlphaGenome scale panel for fairer target-gene ranking evaluation
3
+ selection:
4
+ n_positive_regions: 50
5
+ rule: Select positive regions by positive count, max absolute effect, max distance,
6
+ and min FDR; include all labeled candidate genes for each selected region.
7
+ output: data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top50_pairs.parquet
8
+ csv_output: data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top50_pairs.csv
9
+ summary:
10
+ n_pairs: 669
11
+ n_regions: 50
12
+ n_genes: 592
13
+ n_positive: 111
14
+ n_negative: 558
15
+ prevalence: 0.16591928251121077
16
+ n_non_nearest: 626
17
+ n_midrange_100_500kb: 270
18
+ terms_note: Panel contains benchmark coordinates and labels only. Returned model outputs
19
+ must remain no-training oracle features unless explicit terms review allows training.
data/processed/s2t/gasperini_gse120861/features/external_e2g/encode_re2g_k562_extended_full_feature_metadata.csv ADDED
@@ -0,0 +1,47 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ raw_feature_column,output_feature_column,source_path,terms_ok_for_training,source_name,accession,model_label,released_score_included
2
+ isSelfPromoter,k562_re2g_is_self_promoter,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
3
+ distanceToTSS.Feature,k562_re2g_distancetotss,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
4
+ activity_enh.Feature,k562_re2g_activity_enh,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
5
+ 3DContact.Feature,k562_re2g_3dcontact,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
6
+ activity_prom.Feature,k562_re2g_activity_prom,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
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+ ABCNumerator.Feature,k562_re2g_abcnumerator,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
8
+ ABCScore.Feature,k562_re2g_abcscore,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
9
+ ABCDenominator.Feature,k562_re2g_abcdenominator,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
10
+ normalizedDNase_enh.Feature,k562_re2g_normalizeddnase_enh,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
11
+ normalizedDNase_prom.Feature,k562_re2g_normalizeddnase_prom,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
12
+ normalizedH3K27ac_enh.Feature,k562_re2g_normalizedh3k27ac_enh,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
13
+ normalizedH3K27ac_prom.Feature,k562_re2g_normalizedh3k27ac_prom,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
14
+ numCandidateEnhGene.Feature,k562_re2g_numcandidateenhgene,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
15
+ numTSSEnhGene.Feature,k562_re2g_numtssenhgene,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
16
+ numNearbyEnhancers.Feature,k562_re2g_numnearbyenhancers,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
17
+ sumNearbyEnhancers.Feature,k562_re2g_sumnearbyenhancers,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
18
+ ubiquitousExpressedGene.Feature,k562_re2g_ubiquitousexpressedgene,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
19
+ P2PromoterClass.Feature,k562_re2g_p2promoterclass,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
20
+ averageCorrWeighted.Feature,k562_re2g_averagecorrweighted,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
21
+ H3K4me3_e_max_L_8.Feature,k562_re2g_h3k4me3_e_max_l_8,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
22
+ H3K4me3_e_grad_max_L_8.Feature,k562_re2g_h3k4me3_e_grad_max_l_8,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
23
+ H3K27ac_e_grad_max_L_8.Feature,k562_re2g_h3k27ac_e_grad_max_l_8,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
24
+ DNase_e_grad_max_L_8.Feature,k562_re2g_dnase_e_grad_max_l_8,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
25
+ H3K4me3_e_grad_min_L_8.Feature,k562_re2g_h3k4me3_e_grad_min_l_8,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
26
+ H3K27ac_e_grad_min_L_8.Feature,k562_re2g_h3k27ac_e_grad_min_l_8,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
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30
+ H3K27ac_p_grad_max_L_8.Feature,k562_re2g_h3k27ac_p_grad_max_l_8,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
31
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+ EpiMapScore.Feature,k562_re2g_epimapscore,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
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+ glsCoefficient.Feature,k562_re2g_glscoefficient,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
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+ PEToutsideNormalized.Feature,k562_re2g_petoutsidenormalized,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
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+ promCTCF.Feature,k562_re2g_promctcf,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
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+ enhCTCF.Feature,k562_re2g_enhctcf,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
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+ HiCLoopOutsideNormalized.Feature,k562_re2g_hicloopoutsidenormalized,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
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+ HiCLoopCrossNormalized.Feature,k562_re2g_hicloopcrossnormalized,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
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+ inCCD.Feature,k562_re2g_inccd,data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed,True,encode_re2g_k562_extended_full,ENCFF950FTI,Extended,False
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data/processed/s2t/gasperini_gse120861/features/external_e2g/encode_re2g_k562_extended_full_features.parquet ADDED
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data/processed/s2t/gasperini_gse120861/features/external_e2g/external_e2g_feature_build_summary.csv ADDED
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+ source_name,accession,feature_rows,feature_columns,candidate_pairs_with_overlap,features_path,metadata_path
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data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_feature_metadata.csv ADDED
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+ raw_feature_column,output_feature_column,source_path,terms_ok_for_training
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13
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15
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data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet ADDED
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data/processed/s2t/gasperini_gse120861/features/k562_counterfactual_proxy_features.parquet.metadata.yaml ADDED
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1
+ source_features: data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_recomputed_abc_features.parquet
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+ output: data/processed/s2t/gasperini_gse120861/features/k562_counterfactual_proxy_features.parquet
3
+ purpose: Terms-safe public proxy table for AlphaGenome-like enhancer-mask target-promoter
4
+ delta modeling.
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+ n_pairs: 138057
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+ n_features: 156
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+ blocked_columns:
8
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10
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16
+ - k562_fantom5_cage_
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18
+ contains_alphagenome_values: false
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+ terms_ok_for_training: true
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+ notes:
21
+ - This table is inspired by AlphaGenome counterfactual behavior but does not contain
22
+ AlphaGenome outputs.
23
+ - Released final external E2G scores are excluded from this proxy table.
data/processed/s2t/gasperini_gse120861/features/k562_counterfactual_proxy_features_v2.metadata.yaml ADDED
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1
+ source_features: data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_recomputed_abc_features.parquet
2
+ output: data/processed/s2t/gasperini_gse120861/features/k562_counterfactual_proxy_features_v2.parquet
3
+ purpose: Terms-safe public proxy table for AlphaGenome-like enhancer-mask target-promoter
4
+ delta modeling.
5
+ n_pairs: 138057
6
+ n_features: 273
7
+ blocked_columns:
8
+ - external_e2g_selected_score
9
+ public_prefixes:
10
+ - k562_re2g_
11
+ - k562_dnase_
12
+ - k562_h3k27ac_
13
+ - k562_ac_
14
+ - k562_reabc_
15
+ - k562_hic_
16
+ - k562_roadmap_
17
+ - k562_fantom5_cage_
18
+ - k562_abc_
19
+ - k562_proxy_
20
+ contains_alphagenome_values: false
21
+ terms_ok_for_training: true
22
+ notes:
23
+ - This table is inspired by AlphaGenome counterfactual behavior but does not contain
24
+ AlphaGenome outputs.
25
+ - Released final external E2G scores are excluded from this proxy table.
data/processed/s2t/gasperini_gse120861/features/k562_counterfactual_proxy_features_v2.parquet.feature_families.csv ADDED
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+ feature_name,families
2
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+ k562_re2g_is_self_promoter,"promoter_activity,re2g_inputs"
6
+ k562_re2g_distancetotss,re2g_inputs
7
+ k562_re2g_activity_enh,re2g_inputs
8
+ k562_re2g_3dcontact,"contact,re2g_inputs"
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+ k562_re2g_activity_prom,"promoter_activity,re2g_inputs"
10
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17
+ k562_re2g_numcandidateenhgene,"re2g_inputs,denominator_competition"
18
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19
+ k562_re2g_numnearbyenhancers,re2g_inputs
20
+ k562_re2g_sumnearbyenhancers,re2g_inputs
21
+ k562_re2g_ubiquitousexpressedgene,re2g_inputs
22
+ k562_re2g_p2promoterclass,"promoter_activity,re2g_inputs"
23
+ k562_re2g_averagecorrweighted,"re2g_inputs,coupling_interactions"
24
+ k562_re2g_h3k4me3_e_max_l_8,re2g_inputs
25
+ k562_re2g_h3k4me3_e_grad_max_l_8,re2g_inputs
26
+ k562_re2g_h3k27ac_e_grad_max_l_8,re2g_inputs
27
+ k562_re2g_dnase_e_grad_max_l_8,re2g_inputs
28
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+ k562_re2g_dnase_e_grad_min_l_8,re2g_inputs
31
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32
+ k562_re2g_h3k4me3_p_grad_max_l_8,re2g_inputs
33
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+ k562_re2g_dnase_p_grad_max_l_8,re2g_inputs
35
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+ k562_re2g_h3k27ac_p_grad_min_l_8,re2g_inputs
37
+ k562_re2g_dnase_p_grad_min_l_8,re2g_inputs
38
+ k562_re2g_epimapscore,re2g_inputs
39
+ k562_re2g_glscoefficient,re2g_inputs
40
+ k562_re2g_petoutsidenormalized,"contact,re2g_inputs"
41
+ k562_re2g_petcrossnormalized,"contact,re2g_inputs"
42
+ k562_re2g_promctcf,re2g_inputs
43
+ k562_re2g_enhctcf,re2g_inputs
44
+ k562_re2g_hicloopoutsidenormalized,"contact,re2g_inputs"
45
+ k562_re2g_hicloopcrossnormalized,"contact,re2g_inputs"
46
+ k562_re2g_intad,"contact,re2g_inputs"
47
+ k562_re2g_inccd,re2g_inputs
48
+ k562_re2g_normalizedep300_enh,re2g_inputs
49
+ k562_re2g_activity_enh_squared,re2g_inputs
50
+ k562_re2g_3dcontact_squared,"contact,re2g_inputs"
51
+ k562_abc_has_overlap,other_public
52
+ k562_abc_link_count_log1p,other_public
53
+ k562_abc_max_overlap_bp_log1p,other_public
54
+ k562_abc_activity_base,other_public
55
+ k562_abc_targetgenetss,other_public
56
+ k562_abc_targetgeneexpression,expression_power
57
+ k562_abc_targetgenepromoteractivityquantile,promoter_activity
58
+ k562_abc_targetgeneisexpressed,other_public
59
+ k562_abc_distance,other_public
60
+ k562_abc_isselfpromoter,promoter_activity
61
+ k562_abc_hic_contact,contact
62
+ k562_abc_powerlaw_contact,"contact,expression_power"
63
+ k562_abc_powerlaw_contact_reference,"contact,expression_power"
64
+ k562_abc_hic_contact_pl_scaled,contact
65
+ k562_abc_hic_pseudocount,contact
66
+ k562_abc_hic_contact_pl_scaled_adj,contact
67
+ k562_abc_abc_score_numerator,other_public
68
+ k562_abc_abc_score,other_public
69
+ k562_abc_powerlaw_score_numerator,expression_power
70
+ k562_abc_powerlaw_score,expression_power
71
+ k562_dnase_ENCFF827NRR_region_mean,other_public
72
+ k562_dnase_ENCFF827NRR_region_max,other_public
73
+ k562_dnase_ENCFF827NRR_region_sum,other_public
74
+ k562_dnase_ENCFF447GZO_region_mean,other_public
75
+ k562_dnase_ENCFF447GZO_region_max,other_public
76
+ k562_dnase_ENCFF447GZO_region_sum,other_public
77
+ k562_h3k27ac_wgEncodeBroadHistoneK562H3k27acStdSig_region_mean,other_public
78
+ k562_h3k27ac_wgEncodeBroadHistoneK562H3k27acStdSig_region_max,other_public
79
+ k562_h3k27ac_wgEncodeBroadHistoneK562H3k27acStdSig_region_sum,other_public
80
+ k562_dnase_ENCFF827NRR_promoter_mean,promoter_activity
81
+ k562_dnase_ENCFF827NRR_promoter_max,promoter_activity
82
+ k562_dnase_ENCFF827NRR_promoter_sum,promoter_activity
83
+ k562_dnase_ENCFF447GZO_promoter_mean,promoter_activity
84
+ k562_dnase_ENCFF447GZO_promoter_max,promoter_activity
85
+ k562_dnase_ENCFF447GZO_promoter_sum,promoter_activity
86
+ k562_h3k27ac_wgEncodeBroadHistoneK562H3k27acStdSig_promoter_mean,promoter_activity
87
+ k562_h3k27ac_wgEncodeBroadHistoneK562H3k27acStdSig_promoter_max,promoter_activity
88
+ k562_h3k27ac_wgEncodeBroadHistoneK562H3k27acStdSig_promoter_sum,promoter_activity
89
+ k562_ac_region_dnase_log1p_mean,other_public
90
+ k562_ac_region_h3k27ac_log1p_mean,other_public
91
+ k562_ac_promoter_dnase_log1p_mean,promoter_activity
92
+ k562_ac_promoter_h3k27ac_log1p_mean,promoter_activity
93
+ k562_ac_region_activity,other_public
94
+ k562_ac_promoter_activity,promoter_activity
95
+ k562_ac_activity_x_promoter,promoter_activity
96
+ k562_ac_contact_decay_10kb,contact
97
+ k562_ac_activity_contact_10kb,"contact,coupling_interactions"
98
+ k562_ac_activity_contact_gene_share_10kb,"contact,denominator_competition,coupling_interactions"
99
+ k562_ac_activity_contact_region_share_10kb,"contact,denominator_competition,coupling_interactions"
100
+ k562_ac_promoter_activity_contact_10kb,"contact,promoter_activity,coupling_interactions"
101
+ k562_ac_promoter_activity_contact_gene_share_10kb,"contact,promoter_activity,denominator_competition,coupling_interactions"
102
+ k562_ac_abc_x_activity_contact_10kb,"contact,coupling_interactions"
103
+ k562_ac_abc_x_activity_contact_gene_share_10kb,"contact,denominator_competition,coupling_interactions"
104
+ k562_ac_contact_decay_100kb,contact
105
+ k562_ac_activity_contact_100kb,"contact,coupling_interactions"
106
+ k562_ac_activity_contact_gene_share_100kb,"contact,denominator_competition,coupling_interactions"
107
+ k562_ac_activity_contact_region_share_100kb,"contact,denominator_competition,coupling_interactions"
108
+ k562_ac_promoter_activity_contact_100kb,"contact,promoter_activity,coupling_interactions"
109
+ k562_ac_promoter_activity_contact_gene_share_100kb,"contact,promoter_activity,denominator_competition,coupling_interactions"
110
+ k562_ac_abc_x_activity_contact_100kb,"contact,coupling_interactions"
111
+ k562_ac_abc_x_activity_contact_gene_share_100kb,"contact,denominator_competition,coupling_interactions"
112
+ k562_ac_contact_decay_1mb,contact
113
+ k562_ac_activity_contact_1mb,"contact,coupling_interactions"
114
+ k562_ac_activity_contact_gene_share_1mb,"contact,denominator_competition,coupling_interactions"
115
+ k562_ac_activity_contact_region_share_1mb,"contact,denominator_competition,coupling_interactions"
116
+ k562_ac_promoter_activity_contact_1mb,"contact,promoter_activity,coupling_interactions"
117
+ k562_ac_promoter_activity_contact_gene_share_1mb,"contact,promoter_activity,denominator_competition,coupling_interactions"
118
+ k562_ac_abc_x_activity_contact_1mb,"contact,coupling_interactions"
119
+ k562_ac_abc_x_activity_contact_gene_share_1mb,"contact,denominator_competition,coupling_interactions"
120
+ k562_reabc_molecular_activity,denominator_competition
121
+ k562_reabc_abc_activity_log1p,denominator_competition
122
+ k562_reabc_activity_hybrid,denominator_competition
123
+ k562_reabc_promoter_activity,"promoter_activity,denominator_competition"
124
+ k562_reabc_observed_contact,"contact,denominator_competition"
125
+ k562_reabc_observed_contact_available,"contact,denominator_competition"
126
+ k562_reabc_source_abc_score,denominator_competition
127
+ k562_reabc_distance_contact_10kb,"contact,denominator_competition"
128
+ k562_reabc_contact_hybrid_10kb,"contact,denominator_competition"
129
+ k562_reabc_contact_fallback_used_10kb,"contact,denominator_competition"
130
+ k562_reabc_molecular_activity_contact_10kb,"contact,denominator_competition,coupling_interactions"
131
+ k562_reabc_molecular_activity_contact_10kb_gene_sum_log1p,"contact,denominator_competition,coupling_interactions"
132
+ k562_reabc_molecular_activity_contact_10kb_gene_share,"contact,denominator_competition,coupling_interactions"
133
+ k562_reabc_molecular_activity_contact_10kb_region_share,"contact,denominator_competition,coupling_interactions"
134
+ k562_reabc_hybrid_activity_contact_10kb,"contact,denominator_competition,coupling_interactions"
135
+ k562_reabc_hybrid_activity_contact_10kb_gene_sum_log1p,"contact,denominator_competition,coupling_interactions"
136
+ k562_reabc_hybrid_activity_contact_10kb_gene_share,"contact,denominator_competition,coupling_interactions"
137
+ k562_reabc_hybrid_activity_contact_10kb_region_share,"contact,denominator_competition,coupling_interactions"
138
+ k562_reabc_promoter_weighted_activity_contact_10kb,"contact,promoter_activity,denominator_competition,coupling_interactions"
139
+ k562_reabc_promoter_weighted_activity_contact_10kb_gene_sum_log1p,"contact,promoter_activity,denominator_competition,coupling_interactions"
140
+ k562_reabc_promoter_weighted_activity_contact_10kb_gene_share,"contact,promoter_activity,denominator_competition,coupling_interactions"
141
+ k562_reabc_promoter_weighted_activity_contact_10kb_region_share,"contact,promoter_activity,denominator_competition,coupling_interactions"
142
+ k562_reabc_abcscore_weighted_activity_contact_10kb,"contact,denominator_competition,coupling_interactions"
143
+ k562_reabc_abcscore_weighted_activity_contact_10kb_gene_sum_log1p,"contact,denominator_competition,coupling_interactions"
144
+ k562_reabc_abcscore_weighted_activity_contact_10kb_gene_share,"contact,denominator_competition,coupling_interactions"
145
+ k562_reabc_abcscore_weighted_activity_contact_10kb_region_share,"contact,denominator_competition,coupling_interactions"
146
+ k562_reabc_distance_contact_100kb,"contact,denominator_competition"
147
+ k562_reabc_contact_hybrid_100kb,"contact,denominator_competition"
148
+ k562_reabc_contact_fallback_used_100kb,"contact,denominator_competition"
149
+ k562_reabc_molecular_activity_contact_100kb,"contact,denominator_competition,coupling_interactions"
150
+ k562_reabc_molecular_activity_contact_100kb_gene_sum_log1p,"contact,denominator_competition,coupling_interactions"
151
+ k562_reabc_molecular_activity_contact_100kb_gene_share,"contact,denominator_competition,coupling_interactions"
152
+ k562_reabc_molecular_activity_contact_100kb_region_share,"contact,denominator_competition,coupling_interactions"
153
+ k562_reabc_hybrid_activity_contact_100kb,"contact,denominator_competition,coupling_interactions"
154
+ k562_reabc_hybrid_activity_contact_100kb_gene_sum_log1p,"contact,denominator_competition,coupling_interactions"
155
+ k562_reabc_hybrid_activity_contact_100kb_gene_share,"contact,denominator_competition,coupling_interactions"
156
+ k562_reabc_hybrid_activity_contact_100kb_region_share,"contact,denominator_competition,coupling_interactions"
157
+ k562_reabc_promoter_weighted_activity_contact_100kb,"contact,promoter_activity,denominator_competition,coupling_interactions"
158
+ k562_reabc_promoter_weighted_activity_contact_100kb_gene_sum_log1p,"contact,promoter_activity,denominator_competition,coupling_interactions"
159
+ k562_reabc_promoter_weighted_activity_contact_100kb_gene_share,"contact,promoter_activity,denominator_competition,coupling_interactions"
160
+ k562_reabc_promoter_weighted_activity_contact_100kb_region_share,"contact,promoter_activity,denominator_competition,coupling_interactions"
161
+ k562_reabc_abcscore_weighted_activity_contact_100kb,"contact,denominator_competition,coupling_interactions"
162
+ k562_reabc_abcscore_weighted_activity_contact_100kb_gene_sum_log1p,"contact,denominator_competition,coupling_interactions"
163
+ k562_reabc_abcscore_weighted_activity_contact_100kb_gene_share,"contact,denominator_competition,coupling_interactions"
164
+ k562_reabc_abcscore_weighted_activity_contact_100kb_region_share,"contact,denominator_competition,coupling_interactions"
165
+ k562_reabc_distance_contact_1mb,"contact,denominator_competition"
166
+ k562_reabc_contact_hybrid_1mb,"contact,denominator_competition"
167
+ k562_reabc_contact_fallback_used_1mb,"contact,denominator_competition"
168
+ k562_reabc_molecular_activity_contact_1mb,"contact,denominator_competition,coupling_interactions"
169
+ k562_reabc_molecular_activity_contact_1mb_gene_sum_log1p,"contact,denominator_competition,coupling_interactions"
170
+ k562_reabc_molecular_activity_contact_1mb_gene_share,"contact,denominator_competition,coupling_interactions"
171
+ k562_reabc_molecular_activity_contact_1mb_region_share,"contact,denominator_competition,coupling_interactions"
172
+ k562_reabc_hybrid_activity_contact_1mb,"contact,denominator_competition,coupling_interactions"
173
+ k562_reabc_hybrid_activity_contact_1mb_gene_sum_log1p,"contact,denominator_competition,coupling_interactions"
174
+ k562_reabc_hybrid_activity_contact_1mb_gene_share,"contact,denominator_competition,coupling_interactions"
175
+ k562_reabc_hybrid_activity_contact_1mb_region_share,"contact,denominator_competition,coupling_interactions"
176
+ k562_reabc_promoter_weighted_activity_contact_1mb,"contact,promoter_activity,denominator_competition,coupling_interactions"
177
+ k562_reabc_promoter_weighted_activity_contact_1mb_gene_sum_log1p,"contact,promoter_activity,denominator_competition,coupling_interactions"
178
+ k562_reabc_promoter_weighted_activity_contact_1mb_gene_share,"contact,promoter_activity,denominator_competition,coupling_interactions"
179
+ k562_reabc_promoter_weighted_activity_contact_1mb_region_share,"contact,promoter_activity,denominator_competition,coupling_interactions"
180
+ k562_reabc_abcscore_weighted_activity_contact_1mb,"contact,denominator_competition,coupling_interactions"
181
+ k562_reabc_abcscore_weighted_activity_contact_1mb_gene_sum_log1p,"contact,denominator_competition,coupling_interactions"
182
+ k562_reabc_abcscore_weighted_activity_contact_1mb_gene_share,"contact,denominator_competition,coupling_interactions"
183
+ k562_reabc_abcscore_weighted_activity_contact_1mb_region_share,"contact,denominator_competition,coupling_interactions"
184
+ k562_hic_observed_contact,contact
185
+ k562_hic_observed_contact_log1p,contact
186
+ k562_hic_observed_contact_available,contact
187
+ k562_hic_resolution_bp,contact
188
+ k562_hic_bin_distance_bp,contact
189
+ k562_hic_bin_distance_log1p,contact
190
+ k562_hic_anchor_distance_bp,contact
191
+ k562_hic_lifted_anchor_available,contact
192
+ k562_proxy_region_activity,other_public
193
+ k562_proxy_promoter_activity,promoter_activity
194
+ k562_proxy_contact_10kb,contact
195
+ k562_proxy_contact_100kb,contact
196
+ k562_proxy_contact_1mb,contact
197
+ k562_proxy_contact_total,contact
198
+ k562_proxy_contact_10kb_share,"contact,denominator_competition"
199
+ k562_proxy_contact_100kb_share,"contact,denominator_competition"
200
+ k562_proxy_contact_1mb_share,"contact,denominator_competition"
201
+ k562_proxy_expression_power,expression_power
202
+ k562_proxy_cage_promoter_log1p,promoter_activity
203
+ k562_proxy_distance_log1p,other_public
204
+ k562_proxy_distance_decay_100kb,other_public
205
+ k562_proxy_distance_regime_near_50kb,other_public
206
+ k562_proxy_distance_regime_mid_50_500kb,other_public
207
+ k562_proxy_distance_regime_distal_500kb_plus,other_public
208
+ k562_proxy_activity_contact_10kb,"contact,coupling_interactions"
209
+ k562_proxy_activity_contact_100kb,"contact,coupling_interactions"
210
+ k562_proxy_activity_contact_1mb,"contact,coupling_interactions"
211
+ k562_proxy_promoter_susceptibility,"promoter_activity,coupling_interactions"
212
+ k562_proxy_promoter_contact_10kb,"contact,promoter_activity"
213
+ k562_proxy_promoter_contact_100kb,"contact,promoter_activity"
214
+ k562_proxy_promoter_contact_1mb,"contact,promoter_activity"
215
+ k562_proxy_promoter_susceptibility_expr,"promoter_activity,coupling_interactions"
216
+ k562_proxy_region_promoter_balance,"promoter_activity,coupling_interactions"
217
+ k562_proxy_mask_delta_promoter_10kb,"promoter_activity,coupling_interactions"
218
+ k562_proxy_mask_delta_promoter_100kb,"promoter_activity,coupling_interactions"
219
+ k562_proxy_mask_delta_promoter_1mb,"promoter_activity,coupling_interactions"
220
+ k562_proxy_expression_weighted_delta_10kb,"expression_power,coupling_interactions"
221
+ k562_proxy_region_promoter_activity_contact_10kb,"contact,promoter_activity,coupling_interactions"
222
+ k562_proxy_region_promoter_activity_contact_100kb,"contact,promoter_activity,coupling_interactions"
223
+ k562_proxy_region_promoter_activity_contact_1mb,"contact,promoter_activity,coupling_interactions"
224
+ k562_proxy_distance_weighted_delta_10kb,coupling_interactions
225
+ k562_proxy_near_delta_10kb,coupling_interactions
226
+ k562_proxy_mid_delta_10kb,coupling_interactions
227
+ k562_proxy_distal_delta_10kb,coupling_interactions
228
+ k562_proxy_expression_high_power,expression_power
229
+ k562_proxy_expression_low_power,expression_power
230
+ k562_proxy_high_power_contact_negative_prior,"contact,expression_power"
231
+ k562_proxy_re2g_target_coupling,"re2g_inputs,coupling_interactions"
232
+ k562_proxy_re2g_promoter_contact,"contact,promoter_activity,re2g_inputs"
233
+ k562_proxy_re2g_enhancer_contact,"contact,re2g_inputs"
234
+ k562_proxy_ctcf_loop_support,"contact,re2g_inputs"
235
+ k562_proxy_mask_delta_promoter_10kb_gene_share,"promoter_activity,denominator_competition,coupling_interactions"
236
+ k562_proxy_mask_delta_promoter_10kb_region_share,"promoter_activity,denominator_competition,coupling_interactions"
237
+ k562_proxy_mask_delta_promoter_10kb_gene_rank_pct,"promoter_activity,denominator_competition,coupling_interactions"
238
+ k562_proxy_mask_delta_promoter_10kb_region_rank_pct,"promoter_activity,denominator_competition,coupling_interactions"
239
+ k562_proxy_mask_delta_promoter_100kb_gene_share,"promoter_activity,denominator_competition,coupling_interactions"
240
+ k562_proxy_mask_delta_promoter_100kb_region_share,"promoter_activity,denominator_competition,coupling_interactions"
241
+ k562_proxy_mask_delta_promoter_100kb_gene_rank_pct,"promoter_activity,denominator_competition,coupling_interactions"
242
+ k562_proxy_mask_delta_promoter_100kb_region_rank_pct,"promoter_activity,denominator_competition,coupling_interactions"
243
+ k562_proxy_expression_weighted_delta_10kb_gene_share,"expression_power,denominator_competition,coupling_interactions"
244
+ k562_proxy_expression_weighted_delta_10kb_region_share,"expression_power,denominator_competition,coupling_interactions"
245
+ k562_proxy_expression_weighted_delta_10kb_gene_rank_pct,"expression_power,denominator_competition,coupling_interactions"
246
+ k562_proxy_expression_weighted_delta_10kb_region_rank_pct,"expression_power,denominator_competition,coupling_interactions"
247
+ k562_proxy_distance_weighted_delta_10kb_gene_share,"denominator_competition,coupling_interactions"
248
+ k562_proxy_distance_weighted_delta_10kb_region_share,"denominator_competition,coupling_interactions"
249
+ k562_proxy_distance_weighted_delta_10kb_gene_rank_pct,"denominator_competition,coupling_interactions"
250
+ k562_proxy_distance_weighted_delta_10kb_region_rank_pct,"denominator_competition,coupling_interactions"
251
+ k562_proxy_near_delta_10kb_gene_share,"denominator_competition,coupling_interactions"
252
+ k562_proxy_near_delta_10kb_region_share,"denominator_competition,coupling_interactions"
253
+ k562_proxy_near_delta_10kb_gene_rank_pct,"denominator_competition,coupling_interactions"
254
+ k562_proxy_near_delta_10kb_region_rank_pct,"denominator_competition,coupling_interactions"
255
+ k562_proxy_mid_delta_10kb_gene_share,"denominator_competition,coupling_interactions"
256
+ k562_proxy_mid_delta_10kb_region_share,"denominator_competition,coupling_interactions"
257
+ k562_proxy_mid_delta_10kb_gene_rank_pct,"denominator_competition,coupling_interactions"
258
+ k562_proxy_mid_delta_10kb_region_rank_pct,"denominator_competition,coupling_interactions"
259
+ k562_proxy_distal_delta_10kb_gene_share,"denominator_competition,coupling_interactions"
260
+ k562_proxy_distal_delta_10kb_region_share,"denominator_competition,coupling_interactions"
261
+ k562_proxy_distal_delta_10kb_gene_rank_pct,"denominator_competition,coupling_interactions"
262
+ k562_proxy_distal_delta_10kb_region_rank_pct,"denominator_competition,coupling_interactions"
263
+ k562_proxy_re2g_target_coupling_gene_share,"re2g_inputs,denominator_competition,coupling_interactions"
264
+ k562_proxy_re2g_target_coupling_region_share,"re2g_inputs,denominator_competition,coupling_interactions"
265
+ k562_proxy_re2g_target_coupling_gene_rank_pct,"re2g_inputs,denominator_competition,coupling_interactions"
266
+ k562_proxy_re2g_target_coupling_region_rank_pct,"re2g_inputs,denominator_competition,coupling_interactions"
267
+ k562_proxy_re2g_promoter_contact_gene_share,"contact,promoter_activity,re2g_inputs,denominator_competition"
268
+ k562_proxy_re2g_promoter_contact_region_share,"contact,promoter_activity,re2g_inputs,denominator_competition"
269
+ k562_proxy_re2g_promoter_contact_gene_rank_pct,"contact,promoter_activity,re2g_inputs,denominator_competition"
270
+ k562_proxy_re2g_promoter_contact_region_rank_pct,"contact,promoter_activity,re2g_inputs,denominator_competition"
271
+ k562_proxy_re2g_enhancer_contact_gene_share,"contact,re2g_inputs,denominator_competition"
272
+ k562_proxy_re2g_enhancer_contact_region_share,"contact,re2g_inputs,denominator_competition"
273
+ k562_proxy_re2g_enhancer_contact_gene_rank_pct,"contact,re2g_inputs,denominator_competition"
274
+ k562_proxy_re2g_enhancer_contact_region_rank_pct,"contact,re2g_inputs,denominator_competition"
data/processed/s2t/gasperini_gse120861/features/k562_counterfactual_proxy_features_v2.parquet.metadata.yaml ADDED
@@ -0,0 +1,24 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source_features: data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_recomputed_abc_features.parquet
2
+ output: data/processed/s2t/gasperini_gse120861/features/k562_counterfactual_proxy_features_v2.parquet
3
+ purpose: Terms-safe public proxy table for AlphaGenome-like enhancer-mask target-promoter
4
+ delta modeling.
5
+ n_pairs: 138057
6
+ n_features: 242
7
+ blocked_columns:
8
+ - external_e2g_selected_score
9
+ public_prefixes:
10
+ - k562_re2g_
11
+ - k562_dnase_
12
+ - k562_h3k27ac_
13
+ - k562_ac_
14
+ - k562_reabc_
15
+ - k562_hic_
16
+ - k562_roadmap_
17
+ - k562_fantom5_cage_
18
+ - k562_abc_
19
+ contains_alphagenome_values: false
20
+ terms_ok_for_training: true
21
+ notes:
22
+ - This table is inspired by AlphaGenome counterfactual behavior but does not contain
23
+ AlphaGenome outputs.
24
+ - Released final external E2G scores are excluded from this proxy table.
data/processed/s2t/gasperini_gse120861/features/k562_expression_feature_metadata.yaml ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: Roadmap Epigenomics RNA-seq expression matrix
2
+ url: https://egg2.wustl.edu/roadmap/data/byDataType/rna/expression/57epigenomes.RPKM.pc.gz
3
+ sample_column: E123
4
+ sample_label: K562
5
+ raw_expression: data/raw/k562_molecular/rna_expression/57epigenomes.RPKM.pc.gz
6
+ gene_output: data/processed/s2t/gasperini_gse120861/features/k562_roadmap_expression_genes.parquet
7
+ pair_output: data/processed/s2t/gasperini_gse120861/features/k562_expression_features.parquet
8
+ merged_output: data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet
9
+ n_candidate_pairs: 138057
10
+ n_expression_genes: 19795
11
+ n_candidate_genes_with_expression: 16806
12
+ feature_columns:
13
+ - k562_roadmap_E123_rpkm
14
+ - k562_roadmap_E123_log1p_rpkm
15
+ - k562_roadmap_E123_expressed_gt_0p1
16
+ - k562_roadmap_E123_expressed_gt_1
17
+ - k562_roadmap_E123_expression_rank_pct
18
+ - k562_roadmap_E123_missing_expression
19
+ terms_tag: public Roadmap/RNA-seq feature; terms_ok_for_training pending final release
20
+ audit
data/processed/s2t/gasperini_gse120861/features/k562_fantom5_cage_feature_metadata.yaml ADDED
@@ -0,0 +1,70 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: FANTOM5 K562 CAGE CTSS hg19
2
+ source_audit: data/external/k562_molecular_sources_audit.yaml
3
+ raw_dir: data/raw/k562_molecular/cage
4
+ gene_output: data/processed/s2t/gasperini_gse120861/features/k562_fantom5_cage_genes.parquet
5
+ pair_output: data/processed/s2t/gasperini_gse120861/features/k562_fantom5_cage_features.parquet
6
+ merged_output: data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet
7
+ windows_bp:
8
+ - 1000
9
+ - 2000
10
+ n_candidate_pairs: 138057
11
+ n_candidate_genes: 17990
12
+ feature_columns:
13
+ - k562_fantom5_cage_CNhs11250_max_1000bp
14
+ - k562_fantom5_cage_CNhs11250_max_2000bp
15
+ - k562_fantom5_cage_CNhs11250_n_sites_1000bp
16
+ - k562_fantom5_cage_CNhs11250_n_sites_2000bp
17
+ - k562_fantom5_cage_CNhs11250_opposite_strand_sum_1000bp
18
+ - k562_fantom5_cage_CNhs11250_opposite_strand_sum_2000bp
19
+ - k562_fantom5_cage_CNhs11250_same_strand_sum_1000bp
20
+ - k562_fantom5_cage_CNhs11250_same_strand_sum_2000bp
21
+ - k562_fantom5_cage_CNhs11250_sum_1000bp
22
+ - k562_fantom5_cage_CNhs11250_sum_2000bp
23
+ - k562_fantom5_cage_CNhs12334_max_1000bp
24
+ - k562_fantom5_cage_CNhs12334_max_2000bp
25
+ - k562_fantom5_cage_CNhs12334_n_sites_1000bp
26
+ - k562_fantom5_cage_CNhs12334_n_sites_2000bp
27
+ - k562_fantom5_cage_CNhs12334_opposite_strand_sum_1000bp
28
+ - k562_fantom5_cage_CNhs12334_opposite_strand_sum_2000bp
29
+ - k562_fantom5_cage_CNhs12334_same_strand_sum_1000bp
30
+ - k562_fantom5_cage_CNhs12334_same_strand_sum_2000bp
31
+ - k562_fantom5_cage_CNhs12334_sum_1000bp
32
+ - k562_fantom5_cage_CNhs12334_sum_2000bp
33
+ - k562_fantom5_cage_CNhs12335_max_1000bp
34
+ - k562_fantom5_cage_CNhs12335_max_2000bp
35
+ - k562_fantom5_cage_CNhs12335_n_sites_1000bp
36
+ - k562_fantom5_cage_CNhs12335_n_sites_2000bp
37
+ - k562_fantom5_cage_CNhs12335_opposite_strand_sum_1000bp
38
+ - k562_fantom5_cage_CNhs12335_opposite_strand_sum_2000bp
39
+ - k562_fantom5_cage_CNhs12335_same_strand_sum_1000bp
40
+ - k562_fantom5_cage_CNhs12335_same_strand_sum_2000bp
41
+ - k562_fantom5_cage_CNhs12335_sum_1000bp
42
+ - k562_fantom5_cage_CNhs12335_sum_2000bp
43
+ - k562_fantom5_cage_CNhs12336_max_1000bp
44
+ - k562_fantom5_cage_CNhs12336_max_2000bp
45
+ - k562_fantom5_cage_CNhs12336_n_sites_1000bp
46
+ - k562_fantom5_cage_CNhs12336_n_sites_2000bp
47
+ - k562_fantom5_cage_CNhs12336_opposite_strand_sum_1000bp
48
+ - k562_fantom5_cage_CNhs12336_opposite_strand_sum_2000bp
49
+ - k562_fantom5_cage_CNhs12336_same_strand_sum_1000bp
50
+ - k562_fantom5_cage_CNhs12336_same_strand_sum_2000bp
51
+ - k562_fantom5_cage_CNhs12336_sum_1000bp
52
+ - k562_fantom5_cage_CNhs12336_sum_2000bp
53
+ sources:
54
+ - sample_id: CNhs11250
55
+ path: data/raw/k562_molecular/cage/chronic myelogenous leukemia cell line:K562.CNhs11250.10454-106G4.hg19.ctss.bed.gz
56
+ n_ctss_rows: 1284412
57
+ - sample_id: CNhs12334
58
+ path: data/raw/k562_molecular/cage/chronic myelogenous leukemia cell line:K562 ENCODE,
59
+ biol_rep1.CNhs12334.10824-111C5.hg19.ctss.bed.gz
60
+ n_ctss_rows: 804272
61
+ - sample_id: CNhs12335
62
+ path: data/raw/k562_molecular/cage/chronic myelogenous leukemia cell line:K562 ENCODE,
63
+ biol_rep2.CNhs12335.10825-111C6.hg19.ctss.bed.gz
64
+ n_ctss_rows: 892902
65
+ - sample_id: CNhs12336
66
+ path: data/raw/k562_molecular/cage/chronic myelogenous leukemia cell line:K562 ENCODE,
67
+ biol_rep3.CNhs12336.10826-111C7.hg19.ctss.bed.gz
68
+ n_ctss_rows: 987583
69
+ terms_tag: FANTOM5 CAGE public source; terms_ok_for_training pending final release
70
+ audit
data/processed/s2t/gasperini_gse120861/features/k562_observed_contact_feature_metadata.csv ADDED
@@ -0,0 +1,9 @@
 
 
 
 
 
 
 
 
 
 
1
+ feature_column,source_path,source_assembly,lifted_anchor_path,resolution_bp,terms_ok_for_training,notes
2
+ k562_hic_observed_contact,data/interim/k562_contacts/ENCFF621AIY.10kb.candidate_pixels.parquet,GRCh38,data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet,10000,True,Observed enhancer-promoter contact feature from binned sparse contact pixels.
3
+ k562_hic_observed_contact_log1p,data/interim/k562_contacts/ENCFF621AIY.10kb.candidate_pixels.parquet,GRCh38,data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet,10000,True,Observed enhancer-promoter contact feature from binned sparse contact pixels.
4
+ k562_hic_observed_contact_available,data/interim/k562_contacts/ENCFF621AIY.10kb.candidate_pixels.parquet,GRCh38,data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet,10000,True,Observed enhancer-promoter contact feature from binned sparse contact pixels.
5
+ k562_hic_resolution_bp,data/interim/k562_contacts/ENCFF621AIY.10kb.candidate_pixels.parquet,GRCh38,data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet,10000,True,Observed enhancer-promoter contact feature from binned sparse contact pixels.
6
+ k562_hic_bin_distance_bp,data/interim/k562_contacts/ENCFF621AIY.10kb.candidate_pixels.parquet,GRCh38,data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet,10000,True,Observed enhancer-promoter contact feature from binned sparse contact pixels.
7
+ k562_hic_bin_distance_log1p,data/interim/k562_contacts/ENCFF621AIY.10kb.candidate_pixels.parquet,GRCh38,data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet,10000,True,Observed enhancer-promoter contact feature from binned sparse contact pixels.
8
+ k562_hic_anchor_distance_bp,data/interim/k562_contacts/ENCFF621AIY.10kb.candidate_pixels.parquet,GRCh38,data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet,10000,True,Observed enhancer-promoter contact feature from binned sparse contact pixels.
9
+ k562_hic_lifted_anchor_available,data/interim/k562_contacts/ENCFF621AIY.10kb.candidate_pixels.parquet,GRCh38,data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet,10000,True,Observed enhancer-promoter contact feature from binned sparse contact pixels.
data/processed/s2t/gasperini_gse120861/features/k562_observed_contact_recomputed_abc_metadata.csv ADDED
@@ -0,0 +1,65 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ feature_column,source_tables,terms_ok_for_training,notes
2
+ k562_reabc_molecular_activity,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
3
+ k562_reabc_abc_activity_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
4
+ k562_reabc_activity_hybrid,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
5
+ k562_reabc_promoter_activity,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
6
+ k562_reabc_observed_contact,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
7
+ k562_reabc_observed_contact_available,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
8
+ k562_reabc_source_abc_score,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
9
+ k562_reabc_distance_contact_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
10
+ k562_reabc_contact_hybrid_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
11
+ k562_reabc_contact_fallback_used_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
12
+ k562_reabc_molecular_activity_contact_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
13
+ k562_reabc_molecular_activity_contact_10kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
14
+ k562_reabc_molecular_activity_contact_10kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
15
+ k562_reabc_molecular_activity_contact_10kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
16
+ k562_reabc_hybrid_activity_contact_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
17
+ k562_reabc_hybrid_activity_contact_10kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
18
+ k562_reabc_hybrid_activity_contact_10kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
19
+ k562_reabc_hybrid_activity_contact_10kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
20
+ k562_reabc_promoter_weighted_activity_contact_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
21
+ k562_reabc_promoter_weighted_activity_contact_10kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
22
+ k562_reabc_promoter_weighted_activity_contact_10kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
23
+ k562_reabc_promoter_weighted_activity_contact_10kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
24
+ k562_reabc_abcscore_weighted_activity_contact_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
25
+ k562_reabc_abcscore_weighted_activity_contact_10kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
26
+ k562_reabc_abcscore_weighted_activity_contact_10kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
27
+ k562_reabc_abcscore_weighted_activity_contact_10kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
28
+ k562_reabc_distance_contact_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
29
+ k562_reabc_contact_hybrid_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
30
+ k562_reabc_contact_fallback_used_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
31
+ k562_reabc_molecular_activity_contact_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
32
+ k562_reabc_molecular_activity_contact_100kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
33
+ k562_reabc_molecular_activity_contact_100kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
34
+ k562_reabc_molecular_activity_contact_100kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
35
+ k562_reabc_hybrid_activity_contact_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
36
+ k562_reabc_hybrid_activity_contact_100kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
37
+ k562_reabc_hybrid_activity_contact_100kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
38
+ k562_reabc_hybrid_activity_contact_100kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
39
+ k562_reabc_promoter_weighted_activity_contact_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
40
+ k562_reabc_promoter_weighted_activity_contact_100kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
41
+ k562_reabc_promoter_weighted_activity_contact_100kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
42
+ k562_reabc_promoter_weighted_activity_contact_100kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
43
+ k562_reabc_abcscore_weighted_activity_contact_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
44
+ k562_reabc_abcscore_weighted_activity_contact_100kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
45
+ k562_reabc_abcscore_weighted_activity_contact_100kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
46
+ k562_reabc_abcscore_weighted_activity_contact_100kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
47
+ k562_reabc_distance_contact_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
48
+ k562_reabc_contact_hybrid_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
49
+ k562_reabc_contact_fallback_used_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
50
+ k562_reabc_molecular_activity_contact_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
51
+ k562_reabc_molecular_activity_contact_1mb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
52
+ k562_reabc_molecular_activity_contact_1mb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
53
+ k562_reabc_molecular_activity_contact_1mb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
54
+ k562_reabc_hybrid_activity_contact_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
55
+ k562_reabc_hybrid_activity_contact_1mb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
56
+ k562_reabc_hybrid_activity_contact_1mb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
57
+ k562_reabc_hybrid_activity_contact_1mb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
58
+ k562_reabc_promoter_weighted_activity_contact_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
59
+ k562_reabc_promoter_weighted_activity_contact_1mb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
60
+ k562_reabc_promoter_weighted_activity_contact_1mb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
61
+ k562_reabc_promoter_weighted_activity_contact_1mb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
62
+ k562_reabc_abcscore_weighted_activity_contact_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
63
+ k562_reabc_abcscore_weighted_activity_contact_1mb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
64
+ k562_reabc_abcscore_weighted_activity_contact_1mb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
65
+ k562_reabc_abcscore_weighted_activity_contact_1mb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_metadata.csv ADDED
@@ -0,0 +1,18 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ raw_feature_column,output_feature_column,source_path,terms_ok_for_training
2
+ activity_base,k562_abc_activity_base,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
3
+ TargetGeneTSS,k562_abc_targetgenetss,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
4
+ TargetGeneExpression,k562_abc_targetgeneexpression,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
5
+ TargetGenePromoterActivityQuantile,k562_abc_targetgenepromoteractivityquantile,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
6
+ TargetGeneIsExpressed,k562_abc_targetgeneisexpressed,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
7
+ distance,k562_abc_distance,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
8
+ isSelfPromoter,k562_abc_isselfpromoter,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
9
+ hic_contact,k562_abc_hic_contact,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
10
+ powerlaw_contact,k562_abc_powerlaw_contact,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
11
+ powerlaw_contact_reference,k562_abc_powerlaw_contact_reference,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
12
+ hic_contact_pl_scaled,k562_abc_hic_contact_pl_scaled,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
13
+ hic_pseudocount,k562_abc_hic_pseudocount,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
14
+ hic_contact_pl_scaled_adj,k562_abc_hic_contact_pl_scaled_adj,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
15
+ ABC.Score.Numerator,k562_abc_abc_score_numerator,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
16
+ ABC.Score,k562_abc_abc_score,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
17
+ powerlaw.Score.Numerator,k562_abc_powerlaw_score_numerator,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
18
+ powerlaw.Score,k562_abc_powerlaw_score,data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz,True
data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_observed_contact_features.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:d92094d80ee19bbbd3e1934b9fd81dd83940625b10b6ba4778825f7494e530ee
3
+ size 91445535
data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_recomputed_abc_metadata.csv ADDED
@@ -0,0 +1,65 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ feature_column,source_tables,terms_ok_for_training,notes
2
+ k562_reabc_molecular_activity,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
3
+ k562_reabc_abc_activity_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
4
+ k562_reabc_activity_hybrid,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
5
+ k562_reabc_promoter_activity,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
6
+ k562_reabc_observed_contact,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
7
+ k562_reabc_observed_contact_available,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
8
+ k562_reabc_source_abc_score,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
9
+ k562_reabc_distance_contact_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
10
+ k562_reabc_contact_hybrid_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
11
+ k562_reabc_contact_fallback_used_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
12
+ k562_reabc_molecular_activity_contact_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
13
+ k562_reabc_molecular_activity_contact_10kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
14
+ k562_reabc_molecular_activity_contact_10kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
15
+ k562_reabc_molecular_activity_contact_10kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
16
+ k562_reabc_hybrid_activity_contact_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
17
+ k562_reabc_hybrid_activity_contact_10kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
18
+ k562_reabc_hybrid_activity_contact_10kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
19
+ k562_reabc_hybrid_activity_contact_10kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
20
+ k562_reabc_promoter_weighted_activity_contact_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
21
+ k562_reabc_promoter_weighted_activity_contact_10kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
22
+ k562_reabc_promoter_weighted_activity_contact_10kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
23
+ k562_reabc_promoter_weighted_activity_contact_10kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
24
+ k562_reabc_abcscore_weighted_activity_contact_10kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
25
+ k562_reabc_abcscore_weighted_activity_contact_10kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
26
+ k562_reabc_abcscore_weighted_activity_contact_10kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
27
+ k562_reabc_abcscore_weighted_activity_contact_10kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
28
+ k562_reabc_distance_contact_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
29
+ k562_reabc_contact_hybrid_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
30
+ k562_reabc_contact_fallback_used_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
31
+ k562_reabc_molecular_activity_contact_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
32
+ k562_reabc_molecular_activity_contact_100kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
33
+ k562_reabc_molecular_activity_contact_100kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
34
+ k562_reabc_molecular_activity_contact_100kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
35
+ k562_reabc_hybrid_activity_contact_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
36
+ k562_reabc_hybrid_activity_contact_100kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
37
+ k562_reabc_hybrid_activity_contact_100kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
38
+ k562_reabc_hybrid_activity_contact_100kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
39
+ k562_reabc_promoter_weighted_activity_contact_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
40
+ k562_reabc_promoter_weighted_activity_contact_100kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
41
+ k562_reabc_promoter_weighted_activity_contact_100kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
42
+ k562_reabc_promoter_weighted_activity_contact_100kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
43
+ k562_reabc_abcscore_weighted_activity_contact_100kb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
44
+ k562_reabc_abcscore_weighted_activity_contact_100kb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
45
+ k562_reabc_abcscore_weighted_activity_contact_100kb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
46
+ k562_reabc_abcscore_weighted_activity_contact_100kb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
47
+ k562_reabc_distance_contact_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
48
+ k562_reabc_contact_hybrid_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
49
+ k562_reabc_contact_fallback_used_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
50
+ k562_reabc_molecular_activity_contact_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
51
+ k562_reabc_molecular_activity_contact_1mb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
52
+ k562_reabc_molecular_activity_contact_1mb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
53
+ k562_reabc_molecular_activity_contact_1mb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
54
+ k562_reabc_hybrid_activity_contact_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
55
+ k562_reabc_hybrid_activity_contact_1mb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
56
+ k562_reabc_hybrid_activity_contact_1mb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
57
+ k562_reabc_hybrid_activity_contact_1mb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
58
+ k562_reabc_promoter_weighted_activity_contact_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
59
+ k562_reabc_promoter_weighted_activity_contact_1mb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
60
+ k562_reabc_promoter_weighted_activity_contact_1mb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
61
+ k562_reabc_promoter_weighted_activity_contact_1mb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
62
+ k562_reabc_abcscore_weighted_activity_contact_1mb,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
63
+ k562_reabc_abcscore_weighted_activity_contact_1mb_gene_sum_log1p,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
64
+ k562_reabc_abcscore_weighted_activity_contact_1mb_gene_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
65
+ k562_reabc_abcscore_weighted_activity_contact_1mb_region_share,data/processed/s2t/gasperini_gse120861/features/k562_re2g_extended_plus_abc_contact_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_molecular_features.parquet;data/processed/s2t/gasperini_gse120861/features/k562_abc_contact_features.parquet,True,Exact-candidate ABC/gABC-style denominator feature over Seq2State candidate genes.
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_pilot.parquet.metadata.yaml ADDED
@@ -0,0 +1,18 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: AlphaGenome API K562 enhancer-masking counterfactual
2
+ output: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_pilot.parquet
3
+ pairs: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_pilot_pairs.parquet
4
+ lifted_anchors: data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet
5
+ feature_set: alphagenome_k562_counterfactual_mask_pilot
6
+ ontology_term: EFO:0002067
7
+ mask_base: N
8
+ region_window_bp: 2000
9
+ promoter_window_bp: 2000
10
+ flank_bp: 8192
11
+ n_completed_pairs_loaded: 0
12
+ n_input_pairs: 50
13
+ n_scored_pairs: 50
14
+ n_feature_rows: 1800
15
+ n_failures: 0
16
+ failures: []
17
+ terms_ok_for_training: false
18
+ api_key_stored: false
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_region_complete_all_positive.parquet.metadata.yaml ADDED
@@ -0,0 +1,38 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: AlphaGenome API K562 enhancer-masking counterfactual
2
+ output: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_region_complete_all_positive.parquet
3
+ pairs: data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_all_positive_pairs.parquet
4
+ lifted_anchors: data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet
5
+ feature_set: alphagenome_k562_counterfactual_mask_region_complete_all_positive
6
+ ontology_term: EFO:0002067
7
+ mask_base: N
8
+ region_window_bp: 2000
9
+ promoter_window_bp: 2000
10
+ flank_bp: 8192
11
+ n_completed_pairs_loaded: 2302
12
+ n_input_pairs: 5908
13
+ n_scored_pairs: 5904
14
+ n_feature_rows: 212544
15
+ n_failures: 4
16
+ failures:
17
+ - oracle_request_id: s2f_scale_00132_chr1.12988_top_two_ENSG00000185220
18
+ region_id: chr1.12988_top_two
19
+ gene_id: ENSG00000185220
20
+ error: 'ValueError(''UCSC sequence request failed for chr1:248830107-248961179:
21
+ HTTP Error 400: Bad Request'')'
22
+ - oracle_request_id: s2f_scale_00136_chr1.12989_top_two_ENSG00000185220
23
+ region_id: chr1.12989_top_two
24
+ gene_id: ENSG00000185220
25
+ error: 'ValueError(''UCSC sequence request failed for chr1:248832385-248963457:
26
+ HTTP Error 400: Bad Request'')'
27
+ - oracle_request_id: s2f_scale_00394_chr1.8432_top_two_ENSG00000203817
28
+ region_id: chr1.8432_top_two
29
+ gene_id: ENSG00000203817
30
+ error: ValueError('Pair span 6238367 bp exceeds maximum supported AlphaGenome window
31
+ 1048576 bp')
32
+ - oracle_request_id: s2f_scale_05670_chr9.764_top_two_ENSG00000269337
33
+ region_id: chr9.764_top_two
34
+ gene_id: ENSG00000269337
35
+ error: ValueError('Pair span 27678400 bp exceeds maximum supported AlphaGenome window
36
+ 1048576 bp')
37
+ terms_ok_for_training: false
38
+ api_key_stored: false
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_region_complete_top100.parquet.metadata.yaml ADDED
@@ -0,0 +1,18 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: AlphaGenome API K562 enhancer-masking counterfactual
2
+ output: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_region_complete_top100.parquet
3
+ pairs: data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top100_pairs.parquet
4
+ lifted_anchors: data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet
5
+ feature_set: alphagenome_k562_counterfactual_mask_region_complete_top100
6
+ ontology_term: EFO:0002067
7
+ mask_base: N
8
+ region_window_bp: 2000
9
+ promoter_window_bp: 2000
10
+ flank_bp: 8192
11
+ n_completed_pairs_loaded: 669
12
+ n_input_pairs: 1063
13
+ n_scored_pairs: 1063
14
+ n_feature_rows: 38268
15
+ n_failures: 0
16
+ failures: []
17
+ terms_ok_for_training: false
18
+ api_key_stored: false
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_region_complete_top250.parquet.metadata.yaml ADDED
@@ -0,0 +1,18 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: AlphaGenome API K562 enhancer-masking counterfactual
2
+ output: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_region_complete_top250.parquet
3
+ pairs: data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top250_pairs.parquet
4
+ lifted_anchors: data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet
5
+ feature_set: alphagenome_k562_counterfactual_mask_region_complete_top250
6
+ ontology_term: EFO:0002067
7
+ mask_base: N
8
+ region_window_bp: 2000
9
+ promoter_window_bp: 2000
10
+ flank_bp: 8192
11
+ n_completed_pairs_loaded: 1063
12
+ n_input_pairs: 2302
13
+ n_scored_pairs: 2302
14
+ n_feature_rows: 82872
15
+ n_failures: 0
16
+ failures: []
17
+ terms_ok_for_training: false
18
+ api_key_stored: false
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_region_complete_top50.parquet.metadata.yaml ADDED
@@ -0,0 +1,18 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: AlphaGenome API K562 enhancer-masking counterfactual
2
+ output: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_region_complete_top50.parquet
3
+ pairs: data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top50_pairs.parquet
4
+ lifted_anchors: data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet
5
+ feature_set: alphagenome_k562_counterfactual_mask_region_complete_top50
6
+ ontology_term: EFO:0002067
7
+ mask_base: N
8
+ region_window_bp: 2000
9
+ promoter_window_bp: 2000
10
+ flank_bp: 8192
11
+ n_completed_pairs_loaded: 0
12
+ n_input_pairs: 669
13
+ n_scored_pairs: 669
14
+ n_feature_rows: 24084
15
+ n_failures: 0
16
+ failures: []
17
+ terms_ok_for_training: false
18
+ api_key_stored: false
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_smoke.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:5b15494ff552569e51e7a0e2c7e746519e469fcd011a63f1517226a08eae0c5c
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+ size 18073
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_smoke.parquet.metadata.yaml ADDED
@@ -0,0 +1,18 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: AlphaGenome API K562 enhancer-masking counterfactual
2
+ output: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_counterfactual_smoke.parquet
3
+ pairs: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_pilot_pairs.parquet
4
+ lifted_anchors: data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet
5
+ feature_set: alphagenome_k562_counterfactual_mask_pilot
6
+ ontology_term: EFO:0002067
7
+ mask_base: N
8
+ region_window_bp: 2000
9
+ promoter_window_bp: 2000
10
+ flank_bp: 8192
11
+ n_completed_pairs_loaded: 0
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+ n_input_pairs: 1
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+ n_scored_pairs: 1
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+ n_feature_rows: 36
15
+ n_failures: 0
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+ failures: []
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+ terms_ok_for_training: false
18
+ api_key_stored: false
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_pilot.parquet.metadata.yaml ADDED
@@ -0,0 +1,15 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: AlphaGenome API K562 reference track pilot
2
+ output: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_pilot.parquet
3
+ pilot_pairs: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_pilot_pairs.parquet
4
+ lifted_anchors: data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet
5
+ ontology_term: EFO:0002067
6
+ region_window_bp: 2000
7
+ promoter_window_bp: 2000
8
+ flank_bp: 8192
9
+ n_input_pairs: 50
10
+ n_scored_pairs: 50
11
+ n_feature_rows: 800
12
+ n_failures: 0
13
+ failures: []
14
+ terms_ok_for_training: false
15
+ api_key_stored: false
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_region_complete_top50.parquet.metadata.yaml ADDED
@@ -0,0 +1,18 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: AlphaGenome API K562 reference track pilot
2
+ output: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_region_complete_top50.parquet
3
+ pilot_pairs: data/processed/s2t/gasperini_gse120861/features/alphagenome_region_complete_top50_pairs.parquet
4
+ lifted_anchors: data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet
5
+ ontology_term: EFO:0002067
6
+ feature_set: alphagenome_k562_region_complete_top50
7
+ resume: true
8
+ n_completed_pairs_loaded: 0
9
+ region_window_bp: 2000
10
+ promoter_window_bp: 2000
11
+ flank_bp: 8192
12
+ n_input_pairs: 669
13
+ n_scored_pairs: 669
14
+ n_feature_rows: 10704
15
+ n_failures: 0
16
+ failures: []
17
+ terms_ok_for_training: false
18
+ api_key_stored: false
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_smoke.parquet.metadata.yaml ADDED
@@ -0,0 +1,15 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: AlphaGenome API K562 reference track pilot
2
+ output: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.alphagenome_smoke.parquet
3
+ pilot_pairs: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_pilot_pairs.parquet
4
+ lifted_anchors: data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet
5
+ ontology_term: EFO:0002067
6
+ region_window_bp: 2000
7
+ promoter_window_bp: 2000
8
+ flank_bp: 8192
9
+ n_input_pairs: 1
10
+ n_scored_pairs: 1
11
+ n_feature_rows: 16
12
+ n_failures: 0
13
+ failures: []
14
+ terms_ok_for_training: false
15
+ api_key_stored: false
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_features.open_model_counterfactual_pilot.parquet.metadata.yaml ADDED
@@ -0,0 +1,11 @@
 
 
 
 
 
 
 
 
 
 
 
 
1
+ backend: MockSequenceModel
2
+ backend_version: 0.1.0
3
+ sequence_source: mock
4
+ feature_set: mocksequencemodel_counterfactual_mask_pilot
5
+ terms_ok_for_training: true
6
+ n_scored_pairs: 40
7
+ n_feature_rows: 1440
8
+ n_failures: 0
9
+ is_mock: true
10
+ warning: MOCK backend is a deterministic placeholder, not a biological predictor;
11
+ do not report mock features as results.
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_pilot_pairs.csv ADDED
@@ -0,0 +1,51 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ oracle_request_id,pilot_bucket,region_id,gene_id,gene_symbol,region_chrom,start,end,region_center,chrom,tss,strand,distance_to_tss,abs_distance_to_tss,is_nearest_gene,label_binary,signed_effect,fdr,assembly,suggested_sequence_window_bp,suggested_region_mask_bp,oracle_status
2
+ s2f_0001_chr22.1257_top_two_ENSG00000182541,non_nearest_positive,chr22.1257_top_two,ENSG00000182541,LIMK2,chr22,30612533,30613178,30612855,chr22,31608260,+,995405,995405.0,False,1,-0.361416823777988,0.0873207087449393,hg19,1048576,645,pending_external_model_score
3
+ s2f_0002_chr22.431_top_two_ENSG00000070371,non_nearest_positive,chr22.431_top_two,ENSG00000070371,CLTCL1,chr22,20175500,20176203,20175851,chr22,19195183,-,-980668,980668.0,False,1,-0.751648594917321,0.0671307930668983,hg19,1048576,703,pending_external_model_score
4
+ s2f_0003_chr11.1735_top_two_ENSG00000149089,non_nearest_positive,chr11.1735_top_two,ENSG00000149089,APIP,chr11,33966182,33966805,33966493,chr11,34938045,-,971552,971552.0,False,1,-0.233729704870435,0.0271764628666667,hg19,1048576,623,pending_external_model_score
5
+ s2f_0004_chr19.4185_top_two_ENSG00000090932,non_nearest_positive,chr19.4185_top_two,ENSG00000090932,DLL3,chr19,40941209,40941473,40941341,chr19,39989535,+,-951806,951806.0,False,1,-0.0142671333910385,0.0088235025672877,hg19,1048576,264,pending_external_model_score
6
+ s2f_0005_chr2.2992_top_two_ENSG00000034510,non_nearest_positive,chr2.2992_top_two,ENSG00000034510,TMSB10,chr2,84196225,84196543,84196384,chr2,85132749,+,936365,936365.0,False,1,-0.0810678653006618,0.0834740007920792,hg19,1048576,318,pending_external_model_score
7
+ s2f_0006_chr1.4865_top_two_ENSG00000134698,non_nearest_positive,chr1.4865_top_two,ENSG00000134698,AGO4,chr1,37209434,37209566,37209500,chr1,36273773,+,-935727,935727.0,False,1,-0.674491480288617,0.0979533595975232,hg19,1048576,132,pending_external_model_score
8
+ s2f_0007_chr20.2047_top_two_ENSG00000158296,non_nearest_positive,chr20.2047_top_two,ENSG00000158296,SLC13A3,chr20,46129547,46129619,46129583,chr20,45242524,-,-887059,887059.0,False,1,-0.695769962314059,0.0427280630596176,hg19,1048576,72,pending_external_model_score
9
+ s2f_0008_chr6.1221_top_two_ENSG00000158406,non_nearest_positive,chr6.1221_top_two,ENSG00000158406,HIST1H4H,chr6,27156121,27157007,27156564,chr6,26285736,-,-870828,870828.0,False,1,-0.166315203101591,0.0855435320228385,hg19,1048576,886,pending_external_model_score
10
+ s2f_0009_chr6.1373_top_two_ENSG00000184357,non_nearest_positive,chr6.1373_top_two,ENSG00000184357,HIST1H1B,chr6,28696961,28697283,28697122,chr6,27835306,-,-861816,861816.0,False,1,-0.222692725517331,0.0846667037899918,hg19,1048576,322,pending_external_model_score
11
+ s2f_0010_chr6.1219_top_two_ENSG00000158406,non_nearest_positive,chr6.1219_top_two,ENSG00000158406,HIST1H4H,chr6,27144906,27145983,27145444,chr6,26285736,-,-859708,859708.0,False,1,-0.124977868691419,0.069883192233677,hg19,1048576,1077,pending_external_model_score
12
+ s2f_0011_chr12.1559_top_two_ENSG00000167552,non_nearest_positive,chr12.1559_top_two,ENSG00000167552,TUBA1A,chr12,50435293,50436181,50435737,chr12,49582848,-,-852889,852889.0,False,1,-0.348737574284017,0.0561870227756654,hg19,1048576,888,pending_external_model_score
13
+ s2f_0012_chr6.1416_top_two_ENSG00000198315,non_nearest_positive,chr6.1416_top_two,ENSG00000198315,ZKSCAN8,chr6,28960378,28960689,28960533,chr6,28109716,+,-850817,850817.0,False,1,-0.197025777473007,0.0353199485923754,hg19,1048576,311,pending_external_model_score
14
+ s2f_0013_chr11.1734_top_two_ENSG00000121691,midrange_positive,chr11.1734_top_two,ENSG00000121691,CAT,chr11,33963092,33963689,33963390,chr11,34460472,+,497082,497082.0,False,1,-0.1603056740443,0.0654074690140845,hg19,1048576,597,pending_external_model_score
15
+ s2f_0014_chr11.1735_top_two_ENSG00000121691,midrange_positive,chr11.1735_top_two,ENSG00000121691,CAT,chr11,33966182,33966805,33966493,chr11,34460472,+,493979,493979.0,False,1,-0.591999553216344,0.0004072655384615,hg19,1048576,623,pending_external_model_score
16
+ s2f_0015_chr16.4806_top_two_ENSG00000140941,midrange_positive,chr16.4806_top_two,ENSG00000140941,MAP1LC3B,chr16,87905150,87905476,87905313,chr16,87425406,+,-479907,479907.0,False,1,-0.148147803313105,0.0362683489836888,hg19,1048576,326,pending_external_model_score
17
+ s2f_0016_chr19.488_top_two_ENSG00000071655,midrange_positive,chr19.488_top_two,ENSG00000071655,MBD3,chr19,2059423,2060263,2059843,chr19,1585528,-,-474315,474315.0,False,1,-0.176713528836111,0.0814985758672199,hg19,1048576,840,pending_external_model_score
18
+ s2f_0017_chr6.1279_top_two_ENSG00000198315,midrange_positive,chr6.1279_top_two,ENSG00000198315,ZKSCAN8,chr6,27636220,27636738,27636479,chr6,28109716,+,473237,473237.0,False,1,-0.148020853936407,0.0317976967862715,hg19,1048576,518,pending_external_model_score
19
+ s2f_0018_chr19.2299_top_two_ENSG00000123159,midrange_positive,chr19.2299_top_two,ENSG00000123159,GIPC1,chr19,14134328,14134727,14134527,chr19,14606943,-,472416,472416.0,False,1,-0.203579835212795,0.0805625583277592,hg19,1048576,399,pending_external_model_score
20
+ s2f_0019_chr6.1269_top_two_ENSG00000124635,midrange_positive,chr6.1269_top_two,ENSG00000124635,HIST1H2BJ,chr6,27568298,27568470,27568384,chr6,27100528,-,-467856,467856.0,False,1,-0.164089828711385,0.0366985672417983,hg19,1048576,172,pending_external_model_score
21
+ s2f_0020_chr2.185_top_two_ENSG00000143797,midrange_positive,chr2.185_top_two,ENSG00000143797,MBOAT2,chr2,8675906,8677898,8676902,chr2,9143941,-,467039,467039.0,False,1,-0.152549475054094,0.0991934570046083,hg19,1048576,1992,pending_external_model_score
22
+ s2f_0021_chr6.1284_top_two_ENSG00000198315,midrange_positive,chr6.1284_top_two,ENSG00000198315,ZKSCAN8,chr6,27655053,27656441,27655747,chr6,28109716,+,453969,453969.0,False,1,-0.0866460296559003,0.0304914284177215,hg19,1048576,1388,pending_external_model_score
23
+ s2f_0022_chr6.1269_top_two_ENSG00000197903,midrange_positive,chr6.1269_top_two,ENSG00000197903,HIST1H2BK,chr6,27568298,27568470,27568384,chr6,27114576,-,-453808,453808.0,False,1,-0.0866264517365277,0.0674232662748488,hg19,1048576,172,pending_external_model_score
24
+ s2f_0023_chr6.4973_top_two_ENSG00000164442,nearest_positive,chr6.4973_top_two,ENSG00000164442,CITED2,chr6,139969435,139970015,139969725,chr6,139695741,-,-273984,273984.0,True,1,-0.223925316919865,0.0362683489836888,hg19,1048576,580,pending_external_model_score
25
+ s2f_0024_chr6.4971_top_two_ENSG00000164442,nearest_positive,chr6.4971_top_two,ENSG00000164442,CITED2,chr6,139946331,139946994,139946662,chr6,139695741,-,-250921,250921.0,True,1,-0.207218655451039,0.080387148358459,hg19,1048576,663,pending_external_model_score
26
+ s2f_0025_chr3.2983_top_two_ENSG00000179097,nearest_positive,chr3.2983_top_two,ENSG00000179097,HTR1F,chr3,87847164,87847484,87847324,chr3,88039846,+,192522,192522.0,True,1,-0.689720538062841,0.0385307477336449,hg19,1048576,320,pending_external_model_score
27
+ s2f_0026_chr16.1337_top_two_ENSG00000103381,nearest_positive,chr16.1337_top_two,ENSG00000103381,CPPED1,chr16,12706463,12706842,12706652,chr16,12897707,-,191055,191055.0,True,1,-0.329099622684599,0.0362683489836888,hg19,1048576,379,pending_external_model_score
28
+ s2f_0027_chr3.2985_top_two_ENSG00000179097,nearest_positive,chr3.2985_top_two,ENSG00000179097,HTR1F,chr3,87850705,87850892,87850798,chr3,88039846,+,189048,189048.0,True,1,-0.594257369199853,0.0466695328922092,hg19,1048576,187,pending_external_model_score
29
+ s2f_0028_chr11.3769_top_two_ENSG00000172927,nearest_positive,chr11.3769_top_two,ENSG00000172927,MYEOV,chr11,69224596,69225355,69224975,chr11,69061605,+,-163370,163370.0,True,1,-0.174157096238754,0.0978340313685847,hg19,1048576,759,pending_external_model_score
30
+ s2f_0029_chr6.4966_top_two_ENSG00000164442,nearest_positive,chr6.4966_top_two,ENSG00000164442,CITED2,chr6,139855225,139856063,139855644,chr6,139695741,-,-159903,159903.0,True,1,-0.315339689688442,0.0217383879702048,hg19,1048576,838,pending_external_model_score
31
+ s2f_0030_chr3.2860_top_two_ENSG00000163602,nearest_positive,chr3.2860_top_two,ENSG00000163602,RYBP,chr3,72337978,72339214,72338596,chr3,72495771,-,157175,157175.0,True,1,-0.30475947714093,0.0362683489836888,hg19,1048576,1236,pending_external_model_score
32
+ s2f_0031_chr12.1937_top_two_ENSG00000111057,high_conf_negative,chr12.1937_top_two,ENSG00000111057,KRT18,chr12,54342546,54344544,54343545,chr12,53342655,+,-1000890,1000890.0,False,0,-0.0001207437565472,0.999133110639514,hg19,1048576,1998,pending_external_model_score
33
+ s2f_0032_chr16.496_top_two_ENSG00000103145,high_conf_negative,chr16.496_top_two,ENSG00000103145,HCFC1R1,chr16,2072609,2074298,2073453,chr16,3074273,-,1000820,1000820.0,False,0,-0.0231646637841523,0.938010535859667,hg19,1048576,1689,pending_external_model_score
34
+ s2f_0033_chr12.4339_top_two_ENSG00000110917,high_conf_negative,chr12.4339_top_two,ENSG00000110917,MLEC,chr12,122124604,122125360,122124982,chr12,121124672,+,-1000310,1000310.0,False,0,-0.002213305443108,0.994235057051234,hg19,1048576,756,pending_external_model_score
35
+ s2f_0034_chr5.3450_top_two_ENSG00000170445,high_conf_negative,chr5.3450_top_two,ENSG00000170445,HARS,chr5,141070791,141071452,141071121,chr5,140070925,-,-1000196,1000196.0,False,0,-0.0137832891742187,0.970048469626592,hg19,1048576,661,pending_external_model_score
36
+ s2f_0035_chr3.5813_top_two_ENSG00000075711,high_conf_negative,chr3.5813_top_two,ENSG00000075711,DLG1,chr3,195910312,195910780,195910546,chr3,196910728,-,1000182,1000182.0,False,0,-0.0253829436875081,0.949050980743898,hg19,1048576,468,pending_external_model_score
37
+ s2f_0036_chr5.5178_top_two_ENSG00000146090,high_conf_negative,chr5.5178_top_two,ENSG00000146090,RASGEF1C,chr5,180565272,180565670,180565471,chr5,179565348,-,-1000123,1000123.0,False,0,-0.0189047331984459,0.995117321308481,hg19,1048576,398,pending_external_model_score
38
+ s2f_0037_chr11.2920_top_two_ENSG00000168067,high_conf_negative,chr11.2920_top_two,ENSG00000168067,MAP4K2,chr11,63570381,63570812,63570596,chr11,64570712,-,1000116,1000116.0,False,0,-0.0195942617239314,0.986426901930509,hg19,1048576,431,pending_external_model_score
39
+ s2f_0038_chr9.3146_top_two_ENSG00000136811,high_conf_negative,chr9.3146_top_two,ENSG00000136811,ODF2,chr9,132222205,132223673,132222939,chr9,131222838,+,-1000101,1000101.0,False,0,-0.0212928702672393,0.959858893716475,hg19,1048576,1468,pending_external_model_score
40
+ s2f_0039_chr19.1382_top_two_ENSG00000130255,high_conf_negative,chr19.1382_top_two,ENSG00000130255,RPL36,chr19,6674738,6675330,6675034,chr19,5674958,+,-1000076,1000076.0,False,0,-0.0068979621019771,0.966803430214718,hg19,1048576,592,pending_external_model_score
41
+ s2f_0040_chr15.933_top_two_ENSG00000140264,high_conf_negative,chr15.933_top_two,ENSG00000140264,SERF2,chr15,45084835,45085381,45085108,chr15,44085037,+,-1000071,1000071.0,False,0,-0.0019761796529052,0.992836320328934,hg19,1048576,546,pending_external_model_score
42
+ s2f_0041_chr1.4331_top_two_ENSG00000084652,high_conf_negative,chr1.4331_top_two,ENSG00000084652,TXLNA,chr1,31645159,31645416,31645287,chr1,32645287,+,1000000,1000000.0,False,0,-0.0078386548787743,0.99000201476292,hg19,1048576,257,pending_external_model_score
43
+ s2f_0042_chr12.4672_top_two_ENSG00000111358,high_conf_negative,chr12.4672_top_two,ENSG00000111358,GTF2H3,chr12,125117896,125118618,125118257,chr12,124118286,+,-999971,999971.0,False,0,-0.0438247922229662,0.941111080593829,hg19,1048576,722,pending_external_model_score
44
+ s2f_0043_chr10.2250_top_two_ENSG00000079332,midrange_high_conf_negative,chr10.2250_top_two,ENSG00000079332,SAR1A,chr10,72421541,72421712,72421626,chr10,71921670,-,-499956,499956.0,False,0,-0.0201718965581945,0.946641167895524,hg19,1048576,171,pending_external_model_score
45
+ s2f_0044_chr6.4900_top_two_ENSG00000051620,midrange_high_conf_negative,chr6.4900_top_two,ENSG00000051620,HEBP2,chr6,138224883,138224920,138224901,chr6,138724668,+,499767,499767.0,False,0,-0.0141107812549439,0.942500904415179,hg19,1048576,37,pending_external_model_score
46
+ s2f_0045_chr20.1470_top_two_ENSG00000170471,midrange_high_conf_negative,chr20.1470_top_two,ENSG00000170471,RALGAPB,chr20,36601413,36602170,36601791,chr20,37101459,+,499668,499668.0,False,0,-0.0206815079762885,0.977577276518294,hg19,1048576,757,pending_external_model_score
47
+ s2f_0046_chr22.1656_top_two_ENSG00000100348,midrange_high_conf_negative,chr22.1656_top_two,ENSG00000100348,TXN2,chr22,37376763,37377090,37376926,chr22,36877386,-,-499540,499540.0,False,0,-0.0106713661057072,0.951522066882357,hg19,1048576,327,pending_external_model_score
48
+ s2f_0047_chr19.1559_top_two_ENSG00000032444,midrange_high_conf_negative,chr19.1559_top_two,ENSG00000032444,PNPLA6,chr19,8098053,8098796,8098424,chr19,7598890,+,-499534,499534.0,False,0,-0.0094793223154834,0.991495425584279,hg19,1048576,743,pending_external_model_score
49
+ s2f_0048_chr11.5634_top_two_ENSG00000188486,midrange_high_conf_negative,chr11.5634_top_two,ENSG00000188486,H2AFX,chr11,119465373,119465977,119465675,chr11,118966176,-,-499499,499499.0,False,0,-0.0498686911655,0.813156961151458,hg19,1048576,604,pending_external_model_score
50
+ s2f_0049_chr12.281_top_two_ENSG00000089693,midrange_high_conf_negative,chr12.281_top_two,ENSG00000089693,MLF2,chr12,6362342,6362867,6362604,chr12,6862081,-,499477,499477.0,False,0,-0.0031582621229871,0.991140580971799,hg19,1048576,525,pending_external_model_score
51
+ s2f_0050_chr22.1887_top_two_ENSG00000244509,midrange_high_conf_negative,chr22.1887_top_two,ENSG00000244509,APOBEC3C,chr22,38910577,38910985,38910781,chr22,39410088,+,499307,499307.0,False,0,-0.0257298995498582,0.936436690309109,hg19,1048576,408,pending_external_model_score
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_pilot_pairs.metadata.yaml ADDED
@@ -0,0 +1,17 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: Seq2State Gasperini S2T labels and candidate pairs
2
+ purpose: External AlphaGenome/Borzoi/Enformer no-training oracle scoring manifest
3
+ output: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_pilot_pairs.parquet
4
+ csv_output: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_pilot_pairs.csv
5
+ max_pairs: 50
6
+ random_state: 0
7
+ summary:
8
+ n_pairs: 50
9
+ n_regions: 48
10
+ n_genes: 43
11
+ n_positive: 30
12
+ n_non_nearest: 42
13
+ n_midrange_100_500kb: 26
14
+ n_high_conf_negative: 20
15
+ terms_note: This manifest contains candidate coordinates and labels only. Returned
16
+ model outputs must be stored with terms_ok_for_training=false unless explicit terms
17
+ review allows training.
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_requests.alphagenome.jsonl ADDED
@@ -0,0 +1,50 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {"coordinate_assembly": "hg19", "distance_to_tss": 995405, "gene_id": "ENSG00000182541", "gene_symbol": "LIMK2", "model_family": "alphagenome", "oracle_request_id": "s2f_0001_chr22.1257_top_two_ENSG00000182541", "region": {"chrom": "chr22", "end": 30613178, "start": 30612533}, "region_id": "chr22.1257_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr22", "end": 31137143, "start": 30088567}, "strand": "+", "suggested_region_mask_bp": 645, "target_promoter": {"chrom": "chr22", "end": 31609260, "start": 31607260}, "terms_ok_for_training": false}
2
+ {"coordinate_assembly": "hg19", "distance_to_tss": -980668, "gene_id": "ENSG00000070371", "gene_symbol": "CLTCL1", "model_family": "alphagenome", "oracle_request_id": "s2f_0002_chr22.431_top_two_ENSG00000070371", "region": {"chrom": "chr22", "end": 20176203, "start": 20175500}, "region_id": "chr22.431_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr22", "end": 20700139, "start": 19651563}, "strand": "-", "suggested_region_mask_bp": 703, "target_promoter": {"chrom": "chr22", "end": 19196183, "start": 19194183}, "terms_ok_for_training": false}
3
+ {"coordinate_assembly": "hg19", "distance_to_tss": 971552, "gene_id": "ENSG00000149089", "gene_symbol": "APIP", "model_family": "alphagenome", "oracle_request_id": "s2f_0003_chr11.1735_top_two_ENSG00000149089", "region": {"chrom": "chr11", "end": 33966805, "start": 33966182}, "region_id": "chr11.1735_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr11", "end": 34490781, "start": 33442205}, "strand": "-", "suggested_region_mask_bp": 623, "target_promoter": {"chrom": "chr11", "end": 34939045, "start": 34937045}, "terms_ok_for_training": false}
4
+ {"coordinate_assembly": "hg19", "distance_to_tss": -951806, "gene_id": "ENSG00000090932", "gene_symbol": "DLL3", "model_family": "alphagenome", "oracle_request_id": "s2f_0004_chr19.4185_top_two_ENSG00000090932", "region": {"chrom": "chr19", "end": 40941473, "start": 40941209}, "region_id": "chr19.4185_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr19", "end": 41465629, "start": 40417053}, "strand": "+", "suggested_region_mask_bp": 264, "target_promoter": {"chrom": "chr19", "end": 39990535, "start": 39988535}, "terms_ok_for_training": false}
5
+ {"coordinate_assembly": "hg19", "distance_to_tss": 936365, "gene_id": "ENSG00000034510", "gene_symbol": "TMSB10", "model_family": "alphagenome", "oracle_request_id": "s2f_0005_chr2.2992_top_two_ENSG00000034510", "region": {"chrom": "chr2", "end": 84196543, "start": 84196225}, "region_id": "chr2.2992_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr2", "end": 84720672, "start": 83672096}, "strand": "+", "suggested_region_mask_bp": 318, "target_promoter": {"chrom": "chr2", "end": 85133749, "start": 85131749}, "terms_ok_for_training": false}
6
+ {"coordinate_assembly": "hg19", "distance_to_tss": -935727, "gene_id": "ENSG00000134698", "gene_symbol": "AGO4", "model_family": "alphagenome", "oracle_request_id": "s2f_0006_chr1.4865_top_two_ENSG00000134698", "region": {"chrom": "chr1", "end": 37209566, "start": 37209434}, "region_id": "chr1.4865_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr1", "end": 37733788, "start": 36685212}, "strand": "+", "suggested_region_mask_bp": 132, "target_promoter": {"chrom": "chr1", "end": 36274773, "start": 36272773}, "terms_ok_for_training": false}
7
+ {"coordinate_assembly": "hg19", "distance_to_tss": -887059, "gene_id": "ENSG00000158296", "gene_symbol": "SLC13A3", "model_family": "alphagenome", "oracle_request_id": "s2f_0007_chr20.2047_top_two_ENSG00000158296", "region": {"chrom": "chr20", "end": 46129619, "start": 46129547}, "region_id": "chr20.2047_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr20", "end": 46653871, "start": 45605295}, "strand": "-", "suggested_region_mask_bp": 72, "target_promoter": {"chrom": "chr20", "end": 45243524, "start": 45241524}, "terms_ok_for_training": false}
8
+ {"coordinate_assembly": "hg19", "distance_to_tss": -870828, "gene_id": "ENSG00000158406", "gene_symbol": "HIST1H4H", "model_family": "alphagenome", "oracle_request_id": "s2f_0008_chr6.1221_top_two_ENSG00000158406", "region": {"chrom": "chr6", "end": 27157007, "start": 27156121}, "region_id": "chr6.1221_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr6", "end": 27680852, "start": 26632276}, "strand": "-", "suggested_region_mask_bp": 886, "target_promoter": {"chrom": "chr6", "end": 26286736, "start": 26284736}, "terms_ok_for_training": false}
9
+ {"coordinate_assembly": "hg19", "distance_to_tss": -861816, "gene_id": "ENSG00000184357", "gene_symbol": "HIST1H1B", "model_family": "alphagenome", "oracle_request_id": "s2f_0009_chr6.1373_top_two_ENSG00000184357", "region": {"chrom": "chr6", "end": 28697283, "start": 28696961}, "region_id": "chr6.1373_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr6", "end": 29221410, "start": 28172834}, "strand": "-", "suggested_region_mask_bp": 322, "target_promoter": {"chrom": "chr6", "end": 27836306, "start": 27834306}, "terms_ok_for_training": false}
10
+ {"coordinate_assembly": "hg19", "distance_to_tss": -859708, "gene_id": "ENSG00000158406", "gene_symbol": "HIST1H4H", "model_family": "alphagenome", "oracle_request_id": "s2f_0010_chr6.1219_top_two_ENSG00000158406", "region": {"chrom": "chr6", "end": 27145983, "start": 27144906}, "region_id": "chr6.1219_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr6", "end": 27669732, "start": 26621156}, "strand": "-", "suggested_region_mask_bp": 1077, "target_promoter": {"chrom": "chr6", "end": 26286736, "start": 26284736}, "terms_ok_for_training": false}
11
+ {"coordinate_assembly": "hg19", "distance_to_tss": -852889, "gene_id": "ENSG00000167552", "gene_symbol": "TUBA1A", "model_family": "alphagenome", "oracle_request_id": "s2f_0011_chr12.1559_top_two_ENSG00000167552", "region": {"chrom": "chr12", "end": 50436181, "start": 50435293}, "region_id": "chr12.1559_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr12", "end": 50960025, "start": 49911449}, "strand": "-", "suggested_region_mask_bp": 888, "target_promoter": {"chrom": "chr12", "end": 49583848, "start": 49581848}, "terms_ok_for_training": false}
12
+ {"coordinate_assembly": "hg19", "distance_to_tss": -850817, "gene_id": "ENSG00000198315", "gene_symbol": "ZKSCAN8", "model_family": "alphagenome", "oracle_request_id": "s2f_0012_chr6.1416_top_two_ENSG00000198315", "region": {"chrom": "chr6", "end": 28960689, "start": 28960378}, "region_id": "chr6.1416_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr6", "end": 29484821, "start": 28436245}, "strand": "+", "suggested_region_mask_bp": 311, "target_promoter": {"chrom": "chr6", "end": 28110716, "start": 28108716}, "terms_ok_for_training": false}
13
+ {"coordinate_assembly": "hg19", "distance_to_tss": 497082, "gene_id": "ENSG00000121691", "gene_symbol": "CAT", "model_family": "alphagenome", "oracle_request_id": "s2f_0013_chr11.1734_top_two_ENSG00000121691", "region": {"chrom": "chr11", "end": 33963689, "start": 33963092}, "region_id": "chr11.1734_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr11", "end": 34487678, "start": 33439102}, "strand": "+", "suggested_region_mask_bp": 597, "target_promoter": {"chrom": "chr11", "end": 34461472, "start": 34459472}, "terms_ok_for_training": false}
14
+ {"coordinate_assembly": "hg19", "distance_to_tss": 493979, "gene_id": "ENSG00000121691", "gene_symbol": "CAT", "model_family": "alphagenome", "oracle_request_id": "s2f_0014_chr11.1735_top_two_ENSG00000121691", "region": {"chrom": "chr11", "end": 33966805, "start": 33966182}, "region_id": "chr11.1735_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr11", "end": 34490781, "start": 33442205}, "strand": "+", "suggested_region_mask_bp": 623, "target_promoter": {"chrom": "chr11", "end": 34461472, "start": 34459472}, "terms_ok_for_training": false}
15
+ {"coordinate_assembly": "hg19", "distance_to_tss": -479907, "gene_id": "ENSG00000140941", "gene_symbol": "MAP1LC3B", "model_family": "alphagenome", "oracle_request_id": "s2f_0015_chr16.4806_top_two_ENSG00000140941", "region": {"chrom": "chr16", "end": 87905476, "start": 87905150}, "region_id": "chr16.4806_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr16", "end": 88429601, "start": 87381025}, "strand": "+", "suggested_region_mask_bp": 326, "target_promoter": {"chrom": "chr16", "end": 87426406, "start": 87424406}, "terms_ok_for_training": false}
16
+ {"coordinate_assembly": "hg19", "distance_to_tss": -474315, "gene_id": "ENSG00000071655", "gene_symbol": "MBD3", "model_family": "alphagenome", "oracle_request_id": "s2f_0016_chr19.488_top_two_ENSG00000071655", "region": {"chrom": "chr19", "end": 2060263, "start": 2059423}, "region_id": "chr19.488_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr19", "end": 2584131, "start": 1535555}, "strand": "-", "suggested_region_mask_bp": 840, "target_promoter": {"chrom": "chr19", "end": 1586528, "start": 1584528}, "terms_ok_for_training": false}
17
+ {"coordinate_assembly": "hg19", "distance_to_tss": 473237, "gene_id": "ENSG00000198315", "gene_symbol": "ZKSCAN8", "model_family": "alphagenome", "oracle_request_id": "s2f_0017_chr6.1279_top_two_ENSG00000198315", "region": {"chrom": "chr6", "end": 27636738, "start": 27636220}, "region_id": "chr6.1279_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr6", "end": 28160767, "start": 27112191}, "strand": "+", "suggested_region_mask_bp": 518, "target_promoter": {"chrom": "chr6", "end": 28110716, "start": 28108716}, "terms_ok_for_training": false}
18
+ {"coordinate_assembly": "hg19", "distance_to_tss": 472416, "gene_id": "ENSG00000123159", "gene_symbol": "GIPC1", "model_family": "alphagenome", "oracle_request_id": "s2f_0018_chr19.2299_top_two_ENSG00000123159", "region": {"chrom": "chr19", "end": 14134727, "start": 14134328}, "region_id": "chr19.2299_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr19", "end": 14658815, "start": 13610239}, "strand": "-", "suggested_region_mask_bp": 399, "target_promoter": {"chrom": "chr19", "end": 14607943, "start": 14605943}, "terms_ok_for_training": false}
19
+ {"coordinate_assembly": "hg19", "distance_to_tss": -467856, "gene_id": "ENSG00000124635", "gene_symbol": "HIST1H2BJ", "model_family": "alphagenome", "oracle_request_id": "s2f_0019_chr6.1269_top_two_ENSG00000124635", "region": {"chrom": "chr6", "end": 27568470, "start": 27568298}, "region_id": "chr6.1269_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr6", "end": 28092672, "start": 27044096}, "strand": "-", "suggested_region_mask_bp": 172, "target_promoter": {"chrom": "chr6", "end": 27101528, "start": 27099528}, "terms_ok_for_training": false}
20
+ {"coordinate_assembly": "hg19", "distance_to_tss": 467039, "gene_id": "ENSG00000143797", "gene_symbol": "MBOAT2", "model_family": "alphagenome", "oracle_request_id": "s2f_0020_chr2.185_top_two_ENSG00000143797", "region": {"chrom": "chr2", "end": 8677898, "start": 8675906}, "region_id": "chr2.185_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr2", "end": 9201190, "start": 8152614}, "strand": "-", "suggested_region_mask_bp": 1992, "target_promoter": {"chrom": "chr2", "end": 9144941, "start": 9142941}, "terms_ok_for_training": false}
21
+ {"coordinate_assembly": "hg19", "distance_to_tss": 453969, "gene_id": "ENSG00000198315", "gene_symbol": "ZKSCAN8", "model_family": "alphagenome", "oracle_request_id": "s2f_0021_chr6.1284_top_two_ENSG00000198315", "region": {"chrom": "chr6", "end": 27656441, "start": 27655053}, "region_id": "chr6.1284_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr6", "end": 28180035, "start": 27131459}, "strand": "+", "suggested_region_mask_bp": 1388, "target_promoter": {"chrom": "chr6", "end": 28110716, "start": 28108716}, "terms_ok_for_training": false}
22
+ {"coordinate_assembly": "hg19", "distance_to_tss": -453808, "gene_id": "ENSG00000197903", "gene_symbol": "HIST1H2BK", "model_family": "alphagenome", "oracle_request_id": "s2f_0022_chr6.1269_top_two_ENSG00000197903", "region": {"chrom": "chr6", "end": 27568470, "start": 27568298}, "region_id": "chr6.1269_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr6", "end": 28092672, "start": 27044096}, "strand": "-", "suggested_region_mask_bp": 172, "target_promoter": {"chrom": "chr6", "end": 27115576, "start": 27113576}, "terms_ok_for_training": false}
23
+ {"coordinate_assembly": "hg19", "distance_to_tss": -273984, "gene_id": "ENSG00000164442", "gene_symbol": "CITED2", "model_family": "alphagenome", "oracle_request_id": "s2f_0023_chr6.4973_top_two_ENSG00000164442", "region": {"chrom": "chr6", "end": 139970015, "start": 139969435}, "region_id": "chr6.4973_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr6", "end": 140494013, "start": 139445437}, "strand": "-", "suggested_region_mask_bp": 580, "target_promoter": {"chrom": "chr6", "end": 139696741, "start": 139694741}, "terms_ok_for_training": false}
24
+ {"coordinate_assembly": "hg19", "distance_to_tss": -250921, "gene_id": "ENSG00000164442", "gene_symbol": "CITED2", "model_family": "alphagenome", "oracle_request_id": "s2f_0024_chr6.4971_top_two_ENSG00000164442", "region": {"chrom": "chr6", "end": 139946994, "start": 139946331}, "region_id": "chr6.4971_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr6", "end": 140470950, "start": 139422374}, "strand": "-", "suggested_region_mask_bp": 663, "target_promoter": {"chrom": "chr6", "end": 139696741, "start": 139694741}, "terms_ok_for_training": false}
25
+ {"coordinate_assembly": "hg19", "distance_to_tss": 192522, "gene_id": "ENSG00000179097", "gene_symbol": "HTR1F", "model_family": "alphagenome", "oracle_request_id": "s2f_0025_chr3.2983_top_two_ENSG00000179097", "region": {"chrom": "chr3", "end": 87847484, "start": 87847164}, "region_id": "chr3.2983_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr3", "end": 88371612, "start": 87323036}, "strand": "+", "suggested_region_mask_bp": 320, "target_promoter": {"chrom": "chr3", "end": 88040846, "start": 88038846}, "terms_ok_for_training": false}
26
+ {"coordinate_assembly": "hg19", "distance_to_tss": 191055, "gene_id": "ENSG00000103381", "gene_symbol": "CPPED1", "model_family": "alphagenome", "oracle_request_id": "s2f_0026_chr16.1337_top_two_ENSG00000103381", "region": {"chrom": "chr16", "end": 12706842, "start": 12706463}, "region_id": "chr16.1337_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr16", "end": 13230940, "start": 12182364}, "strand": "-", "suggested_region_mask_bp": 379, "target_promoter": {"chrom": "chr16", "end": 12898707, "start": 12896707}, "terms_ok_for_training": false}
27
+ {"coordinate_assembly": "hg19", "distance_to_tss": 189048, "gene_id": "ENSG00000179097", "gene_symbol": "HTR1F", "model_family": "alphagenome", "oracle_request_id": "s2f_0027_chr3.2985_top_two_ENSG00000179097", "region": {"chrom": "chr3", "end": 87850892, "start": 87850705}, "region_id": "chr3.2985_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr3", "end": 88375086, "start": 87326510}, "strand": "+", "suggested_region_mask_bp": 187, "target_promoter": {"chrom": "chr3", "end": 88040846, "start": 88038846}, "terms_ok_for_training": false}
28
+ {"coordinate_assembly": "hg19", "distance_to_tss": -163370, "gene_id": "ENSG00000172927", "gene_symbol": "MYEOV", "model_family": "alphagenome", "oracle_request_id": "s2f_0028_chr11.3769_top_two_ENSG00000172927", "region": {"chrom": "chr11", "end": 69225355, "start": 69224596}, "region_id": "chr11.3769_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr11", "end": 69749263, "start": 68700687}, "strand": "+", "suggested_region_mask_bp": 759, "target_promoter": {"chrom": "chr11", "end": 69062605, "start": 69060605}, "terms_ok_for_training": false}
29
+ {"coordinate_assembly": "hg19", "distance_to_tss": -159903, "gene_id": "ENSG00000164442", "gene_symbol": "CITED2", "model_family": "alphagenome", "oracle_request_id": "s2f_0029_chr6.4966_top_two_ENSG00000164442", "region": {"chrom": "chr6", "end": 139856063, "start": 139855225}, "region_id": "chr6.4966_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr6", "end": 140379932, "start": 139331356}, "strand": "-", "suggested_region_mask_bp": 838, "target_promoter": {"chrom": "chr6", "end": 139696741, "start": 139694741}, "terms_ok_for_training": false}
30
+ {"coordinate_assembly": "hg19", "distance_to_tss": 157175, "gene_id": "ENSG00000163602", "gene_symbol": "RYBP", "model_family": "alphagenome", "oracle_request_id": "s2f_0030_chr3.2860_top_two_ENSG00000163602", "region": {"chrom": "chr3", "end": 72339214, "start": 72337978}, "region_id": "chr3.2860_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr3", "end": 72862884, "start": 71814308}, "strand": "-", "suggested_region_mask_bp": 1236, "target_promoter": {"chrom": "chr3", "end": 72496771, "start": 72494771}, "terms_ok_for_training": false}
31
+ {"coordinate_assembly": "hg19", "distance_to_tss": -1000890, "gene_id": "ENSG00000111057", "gene_symbol": "KRT18", "model_family": "alphagenome", "oracle_request_id": "s2f_0031_chr12.1937_top_two_ENSG00000111057", "region": {"chrom": "chr12", "end": 54344544, "start": 54342546}, "region_id": "chr12.1937_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr12", "end": 54867833, "start": 53819257}, "strand": "+", "suggested_region_mask_bp": 1998, "target_promoter": {"chrom": "chr12", "end": 53343655, "start": 53341655}, "terms_ok_for_training": false}
32
+ {"coordinate_assembly": "hg19", "distance_to_tss": 1000820, "gene_id": "ENSG00000103145", "gene_symbol": "HCFC1R1", "model_family": "alphagenome", "oracle_request_id": "s2f_0032_chr16.496_top_two_ENSG00000103145", "region": {"chrom": "chr16", "end": 2074298, "start": 2072609}, "region_id": "chr16.496_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr16", "end": 2597741, "start": 1549165}, "strand": "-", "suggested_region_mask_bp": 1689, "target_promoter": {"chrom": "chr16", "end": 3075273, "start": 3073273}, "terms_ok_for_training": false}
33
+ {"coordinate_assembly": "hg19", "distance_to_tss": -1000310, "gene_id": "ENSG00000110917", "gene_symbol": "MLEC", "model_family": "alphagenome", "oracle_request_id": "s2f_0033_chr12.4339_top_two_ENSG00000110917", "region": {"chrom": "chr12", "end": 122125360, "start": 122124604}, "region_id": "chr12.4339_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr12", "end": 122649270, "start": 121600694}, "strand": "+", "suggested_region_mask_bp": 756, "target_promoter": {"chrom": "chr12", "end": 121125672, "start": 121123672}, "terms_ok_for_training": false}
34
+ {"coordinate_assembly": "hg19", "distance_to_tss": -1000196, "gene_id": "ENSG00000170445", "gene_symbol": "HARS", "model_family": "alphagenome", "oracle_request_id": "s2f_0034_chr5.3450_top_two_ENSG00000170445", "region": {"chrom": "chr5", "end": 141071452, "start": 141070791}, "region_id": "chr5.3450_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr5", "end": 141595409, "start": 140546833}, "strand": "-", "suggested_region_mask_bp": 661, "target_promoter": {"chrom": "chr5", "end": 140071925, "start": 140069925}, "terms_ok_for_training": false}
35
+ {"coordinate_assembly": "hg19", "distance_to_tss": 1000182, "gene_id": "ENSG00000075711", "gene_symbol": "DLG1", "model_family": "alphagenome", "oracle_request_id": "s2f_0035_chr3.5813_top_two_ENSG00000075711", "region": {"chrom": "chr3", "end": 195910780, "start": 195910312}, "region_id": "chr3.5813_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr3", "end": 196434834, "start": 195386258}, "strand": "-", "suggested_region_mask_bp": 468, "target_promoter": {"chrom": "chr3", "end": 196911728, "start": 196909728}, "terms_ok_for_training": false}
36
+ {"coordinate_assembly": "hg19", "distance_to_tss": -1000123, "gene_id": "ENSG00000146090", "gene_symbol": "RASGEF1C", "model_family": "alphagenome", "oracle_request_id": "s2f_0036_chr5.5178_top_two_ENSG00000146090", "region": {"chrom": "chr5", "end": 180565670, "start": 180565272}, "region_id": "chr5.5178_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr5", "end": 181089759, "start": 180041183}, "strand": "-", "suggested_region_mask_bp": 398, "target_promoter": {"chrom": "chr5", "end": 179566348, "start": 179564348}, "terms_ok_for_training": false}
37
+ {"coordinate_assembly": "hg19", "distance_to_tss": 1000116, "gene_id": "ENSG00000168067", "gene_symbol": "MAP4K2", "model_family": "alphagenome", "oracle_request_id": "s2f_0037_chr11.2920_top_two_ENSG00000168067", "region": {"chrom": "chr11", "end": 63570812, "start": 63570381}, "region_id": "chr11.2920_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr11", "end": 64094884, "start": 63046308}, "strand": "-", "suggested_region_mask_bp": 431, "target_promoter": {"chrom": "chr11", "end": 64571712, "start": 64569712}, "terms_ok_for_training": false}
38
+ {"coordinate_assembly": "hg19", "distance_to_tss": -1000101, "gene_id": "ENSG00000136811", "gene_symbol": "ODF2", "model_family": "alphagenome", "oracle_request_id": "s2f_0038_chr9.3146_top_two_ENSG00000136811", "region": {"chrom": "chr9", "end": 132223673, "start": 132222205}, "region_id": "chr9.3146_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr9", "end": 132747227, "start": 131698651}, "strand": "+", "suggested_region_mask_bp": 1468, "target_promoter": {"chrom": "chr9", "end": 131223838, "start": 131221838}, "terms_ok_for_training": false}
39
+ {"coordinate_assembly": "hg19", "distance_to_tss": -1000076, "gene_id": "ENSG00000130255", "gene_symbol": "RPL36", "model_family": "alphagenome", "oracle_request_id": "s2f_0039_chr19.1382_top_two_ENSG00000130255", "region": {"chrom": "chr19", "end": 6675330, "start": 6674738}, "region_id": "chr19.1382_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr19", "end": 7199322, "start": 6150746}, "strand": "+", "suggested_region_mask_bp": 592, "target_promoter": {"chrom": "chr19", "end": 5675958, "start": 5673958}, "terms_ok_for_training": false}
40
+ {"coordinate_assembly": "hg19", "distance_to_tss": -1000071, "gene_id": "ENSG00000140264", "gene_symbol": "SERF2", "model_family": "alphagenome", "oracle_request_id": "s2f_0040_chr15.933_top_two_ENSG00000140264", "region": {"chrom": "chr15", "end": 45085381, "start": 45084835}, "region_id": "chr15.933_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr15", "end": 45609396, "start": 44560820}, "strand": "+", "suggested_region_mask_bp": 546, "target_promoter": {"chrom": "chr15", "end": 44086037, "start": 44084037}, "terms_ok_for_training": false}
41
+ {"coordinate_assembly": "hg19", "distance_to_tss": 1000000, "gene_id": "ENSG00000084652", "gene_symbol": "TXLNA", "model_family": "alphagenome", "oracle_request_id": "s2f_0041_chr1.4331_top_two_ENSG00000084652", "region": {"chrom": "chr1", "end": 31645416, "start": 31645159}, "region_id": "chr1.4331_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr1", "end": 32169575, "start": 31120999}, "strand": "+", "suggested_region_mask_bp": 257, "target_promoter": {"chrom": "chr1", "end": 32646287, "start": 32644287}, "terms_ok_for_training": false}
42
+ {"coordinate_assembly": "hg19", "distance_to_tss": -999971, "gene_id": "ENSG00000111358", "gene_symbol": "GTF2H3", "model_family": "alphagenome", "oracle_request_id": "s2f_0042_chr12.4672_top_two_ENSG00000111358", "region": {"chrom": "chr12", "end": 125118618, "start": 125117896}, "region_id": "chr12.4672_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr12", "end": 125642545, "start": 124593969}, "strand": "+", "suggested_region_mask_bp": 722, "target_promoter": {"chrom": "chr12", "end": 124119286, "start": 124117286}, "terms_ok_for_training": false}
43
+ {"coordinate_assembly": "hg19", "distance_to_tss": -499956, "gene_id": "ENSG00000079332", "gene_symbol": "SAR1A", "model_family": "alphagenome", "oracle_request_id": "s2f_0043_chr10.2250_top_two_ENSG00000079332", "region": {"chrom": "chr10", "end": 72421712, "start": 72421541}, "region_id": "chr10.2250_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr10", "end": 72945914, "start": 71897338}, "strand": "-", "suggested_region_mask_bp": 171, "target_promoter": {"chrom": "chr10", "end": 71922670, "start": 71920670}, "terms_ok_for_training": false}
44
+ {"coordinate_assembly": "hg19", "distance_to_tss": 499767, "gene_id": "ENSG00000051620", "gene_symbol": "HEBP2", "model_family": "alphagenome", "oracle_request_id": "s2f_0044_chr6.4900_top_two_ENSG00000051620", "region": {"chrom": "chr6", "end": 138224920, "start": 138224883}, "region_id": "chr6.4900_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr6", "end": 138749189, "start": 137700613}, "strand": "+", "suggested_region_mask_bp": 37, "target_promoter": {"chrom": "chr6", "end": 138725668, "start": 138723668}, "terms_ok_for_training": false}
45
+ {"coordinate_assembly": "hg19", "distance_to_tss": 499668, "gene_id": "ENSG00000170471", "gene_symbol": "RALGAPB", "model_family": "alphagenome", "oracle_request_id": "s2f_0045_chr20.1470_top_two_ENSG00000170471", "region": {"chrom": "chr20", "end": 36602170, "start": 36601413}, "region_id": "chr20.1470_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr20", "end": 37126079, "start": 36077503}, "strand": "+", "suggested_region_mask_bp": 757, "target_promoter": {"chrom": "chr20", "end": 37102459, "start": 37100459}, "terms_ok_for_training": false}
46
+ {"coordinate_assembly": "hg19", "distance_to_tss": -499540, "gene_id": "ENSG00000100348", "gene_symbol": "TXN2", "model_family": "alphagenome", "oracle_request_id": "s2f_0046_chr22.1656_top_two_ENSG00000100348", "region": {"chrom": "chr22", "end": 37377090, "start": 37376763}, "region_id": "chr22.1656_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr22", "end": 37901214, "start": 36852638}, "strand": "-", "suggested_region_mask_bp": 327, "target_promoter": {"chrom": "chr22", "end": 36878386, "start": 36876386}, "terms_ok_for_training": false}
47
+ {"coordinate_assembly": "hg19", "distance_to_tss": -499534, "gene_id": "ENSG00000032444", "gene_symbol": "PNPLA6", "model_family": "alphagenome", "oracle_request_id": "s2f_0047_chr19.1559_top_two_ENSG00000032444", "region": {"chrom": "chr19", "end": 8098796, "start": 8098053}, "region_id": "chr19.1559_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr19", "end": 8622712, "start": 7574136}, "strand": "+", "suggested_region_mask_bp": 743, "target_promoter": {"chrom": "chr19", "end": 7599890, "start": 7597890}, "terms_ok_for_training": false}
48
+ {"coordinate_assembly": "hg19", "distance_to_tss": -499499, "gene_id": "ENSG00000188486", "gene_symbol": "H2AFX", "model_family": "alphagenome", "oracle_request_id": "s2f_0048_chr11.5634_top_two_ENSG00000188486", "region": {"chrom": "chr11", "end": 119465977, "start": 119465373}, "region_id": "chr11.5634_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr11", "end": 119989963, "start": 118941387}, "strand": "-", "suggested_region_mask_bp": 604, "target_promoter": {"chrom": "chr11", "end": 118967176, "start": 118965176}, "terms_ok_for_training": false}
49
+ {"coordinate_assembly": "hg19", "distance_to_tss": 499477, "gene_id": "ENSG00000089693", "gene_symbol": "MLF2", "model_family": "alphagenome", "oracle_request_id": "s2f_0049_chr12.281_top_two_ENSG00000089693", "region": {"chrom": "chr12", "end": 6362867, "start": 6362342}, "region_id": "chr12.281_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr12", "end": 6886892, "start": 5838316}, "strand": "-", "suggested_region_mask_bp": 525, "target_promoter": {"chrom": "chr12", "end": 6863081, "start": 6861081}, "terms_ok_for_training": false}
50
+ {"coordinate_assembly": "hg19", "distance_to_tss": 499307, "gene_id": "ENSG00000244509", "gene_symbol": "APOBEC3C", "model_family": "alphagenome", "oracle_request_id": "s2f_0050_chr22.1887_top_two_ENSG00000244509", "region": {"chrom": "chr22", "end": 38910985, "start": 38910577}, "region_id": "chr22.1887_top_two", "request_status": "ready_for_external_model", "requested_features": ["enhancer_activity", "target_promoter_delta", "chromatin_accessibility_delta", "region_to_promoter_coupling"], "sequence_window": {"chrom": "chr22", "end": 39435069, "start": 38386493}, "strand": "+", "suggested_region_mask_bp": 408, "target_promoter": {"chrom": "chr22", "end": 39411088, "start": 39409088}, "terms_ok_for_training": false}
data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_requests.alphagenome.jsonl.metadata.yaml ADDED
@@ -0,0 +1,14 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_pilot_pairs.parquet
2
+ output: data/processed/s2t/gasperini_gse120861/features/sequence_to_function_oracle_requests.alphagenome.jsonl
3
+ model_family: alphagenome
4
+ sequence_window_bp: null
5
+ promoter_window_bp: 2000
6
+ summary:
7
+ n_requests: 50
8
+ n_regions: 48
9
+ n_genes: 43
10
+ n_assemblies: 1
11
+ n_model_families: 1
12
+ n_terms_ok_for_training: 0
13
+ terms_note: Requests are for no-training oracle evaluation; returned features must
14
+ keep terms_ok_for_training=false unless terms review changes this.
data/processed/s2t/gasperini_gse120861/qc_summary.yaml ADDED
@@ -0,0 +1,12 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ source_dataset: gasperini_gse120861_at_scale
2
+ cell_context: K562
3
+ assembly: hg19
4
+ regions: 6143
5
+ candidate_pairs: 138057
6
+ label_rows: 40322
7
+ positive_labels: 664
8
+ labeled_candidate_pairs: 40322
9
+ labeled_candidate_positive_pairs: 664
10
+ fdr_threshold: 0.1
11
+ quality_rank_grna: top_two
12
+ site_type: DHS
data/processed/s2t/gm12878_heldout/qc_summary.yaml ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ source_dataset: gm12878_heldout
2
+ cell_context: GM12878
3
+ assembly: hg38
4
+ n_regions: 68
5
+ n_candidate_pairs: 68
6
+ n_labeled_pairs: 68
7
+ n_positive_pairs: 16
8
+ prevalence: 0.23529411764705882
data/processed/s2t/hct116_heldout/qc_summary.yaml ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ source_dataset: hct116_heldout
2
+ cell_context: HCT116
3
+ assembly: hg38
4
+ n_regions: 396
5
+ n_candidate_pairs: 396
6
+ n_labeled_pairs: 396
7
+ n_positive_pairs: 34
8
+ prevalence: 0.08585858585858586
data/processed/t2s/vcc_2025/perturbation_response_stats_qc.yaml ADDED
@@ -0,0 +1,10 @@
 
 
 
 
 
 
 
 
 
 
 
1
+ n_input_cells: 221273
2
+ n_response_genes: 18080
3
+ n_control_cells: 38176
4
+ n_perturbations: 150
5
+ n_long_rows: 2712000
6
+ n_top_rows: 15000
7
+ top_n: 100
8
+ control_label: non-targeting
9
+ statistic_note: z_score_delta_expression is delta divided by pseudobulk SEM; no multiple-testing
10
+ model is implied.
data/processed/t2s/vcc_2025/perturbation_signature_qc.yaml ADDED
@@ -0,0 +1,10 @@
 
 
 
 
 
 
 
 
 
 
 
1
+ input_h5ad: data/raw/vcc/2025/train/adata_Training.h5ad
2
+ output_h5ad: data/processed/t2s/vcc_2025/perturbation_signatures.h5ad
3
+ n_input_cells: 221273
4
+ n_input_genes: 18080
5
+ n_signature_perturbations: 150
6
+ n_response_genes: 18080
7
+ control_label: non-targeting
8
+ n_control_cells: 38176
9
+ min_cells_per_perturbation: 20
10
+ skipped_perturbations: []
data/processed/t2s/vcc_2025/smoke_perturbation_signature_qc.yaml ADDED
@@ -0,0 +1,10 @@
 
 
 
 
 
 
 
 
 
 
 
1
+ input_h5ad: data/raw/vcc/2025/train/adata_Training.h5ad
2
+ output_h5ad: data/processed/t2s/vcc_2025/smoke_perturbation_signatures.h5ad
3
+ n_input_cells: 221273
4
+ n_input_genes: 18080
5
+ n_signature_perturbations: 3
6
+ n_response_genes: 18080
7
+ control_label: non-targeting
8
+ n_control_cells: 38176
9
+ min_cells_per_perturbation: 20
10
+ skipped_perturbations: []