Datasets:

ctheodoris
/

Genecorpus-30M

License:

ctheodoris commited on Jun 9, 2023

Commit

eab40d3

1 Parent(s): 7ad207e

Upload example fine-tuning datasets

Browse files

Files changed (15) hide show

example_input_files/cell_classification/cell_type_annotation/cell_type_test_data.dataset/dataset.arrow +3 -0
example_input_files/cell_classification/cell_type_annotation/cell_type_test_data.dataset/dataset_info.json +3 -0
example_input_files/cell_classification/cell_type_annotation/cell_type_test_data.dataset/state.json +3 -0
example_input_files/cell_classification/cell_type_annotation/cell_type_train_data.dataset/dataset.arrow +3 -0
example_input_files/cell_classification/cell_type_annotation/cell_type_train_data.dataset/dataset_info.json +3 -0
example_input_files/cell_classification/cell_type_annotation/cell_type_train_data.dataset/state.json +3 -0
example_input_files/gene_classification/bivalent_promoters/bivalent_gene_labels.txt +107 -0
example_input_files/gene_classification/bivalent_promoters/lys4_only_gene_labels.txt +80 -0
example_input_files/gene_classification/bivalent_promoters/no_methylation_gene_labels.txt +42 -0
example_input_files/gene_classification/bivalent_promoters/panglao_SRA553822-SRS2119548.dataset/dataset.arrow +3 -0
example_input_files/gene_classification/bivalent_promoters/panglao_SRA553822-SRS2119548.dataset/dataset_info.json +3 -0
example_input_files/gene_classification/bivalent_promoters/panglao_SRA553822-SRS2119548.dataset/state.json +3 -0
example_input_files/gene_classification/dosage_sensitive_tfs/README.md +1 -0
example_input_files/gene_classification/dosage_sensitive_tfs/dosage_sens_tf_labels.csv +369 -0
example_input_files/gene_info_table.csv +0 -0

example_input_files/cell_classification/cell_type_annotation/cell_type_test_data.dataset/dataset.arrow ADDED Viewed

	@@ -0,0 +1,3 @@

+version https://git-lfs.github.com/spec/v1
+oid sha256:4f237390758e2a3ad4f4d83e9f2281da5a21a6b6f8b7fc05faf941b9c3a3d65c
+size 1002508240

example_input_files/cell_classification/cell_type_annotation/cell_type_test_data.dataset/dataset_info.json ADDED Viewed

	@@ -0,0 +1,3 @@

+version https://git-lfs.github.com/spec/v1
+oid sha256:aede6907aeb5ff3b02db63c139e001edf09cbd8d7f7ca77a962f78514c4432e3
+size 832

example_input_files/cell_classification/cell_type_annotation/cell_type_test_data.dataset/state.json ADDED Viewed

	@@ -0,0 +1,3 @@

+version https://git-lfs.github.com/spec/v1
+oid sha256:5c4f6e82c4ad22ba62ad16bedb8b8533f793ffcf357d8a13cc893c494201b4c9
+size 383

example_input_files/cell_classification/cell_type_annotation/cell_type_train_data.dataset/dataset.arrow ADDED Viewed

	@@ -0,0 +1,3 @@

+version https://git-lfs.github.com/spec/v1
+oid sha256:b23c9ff672c6648078dbd6274833f68fc89c254905e2503268bbdf95b0170714
+size 938300144

example_input_files/cell_classification/cell_type_annotation/cell_type_train_data.dataset/dataset_info.json ADDED Viewed

	@@ -0,0 +1,3 @@

+version https://git-lfs.github.com/spec/v1
+oid sha256:ca1d81b2fd00f21c6ea673329372da7767f008933e76fa1983fd0f9f5226cc2a
+size 58416

example_input_files/cell_classification/cell_type_annotation/cell_type_train_data.dataset/state.json ADDED Viewed

	@@ -0,0 +1,3 @@

+version https://git-lfs.github.com/spec/v1
+oid sha256:9008170a9b8cf939f6c23a0e41603f23f87cf2eaa06004c67254eed68a348ea5
+size 450

example_input_files/gene_classification/bivalent_promoters/bivalent_gene_labels.txt ADDED Viewed

	@@ -0,0 +1,107 @@

+ENSG00000005073
+ENSG00000007372
+ENSG00000007372
+ENSG00000043355
+ENSG00000068120
+ENSG00000075891
+ENSG00000078399
+ENSG00000105991
+ENSG00000105996
+ENSG00000105997
+ENSG00000106004
+ENSG00000106006
+ENSG00000106031
+ENSG00000106038
+ENSG00000107807
+ENSG00000107821
+ENSG00000107831
+ENSG00000107859
+ENSG00000107862
+ENSG00000108511
+ENSG00000108786
+ENSG00000108797
+ENSG00000110693
+ENSG00000110693
+ENSG00000113430
+ENSG00000115844
+ENSG00000117707
+ENSG00000117707
+ENSG00000119915
+ENSG00000120068
+ENSG00000120075
+ENSG00000120093
+ENSG00000120093
+ENSG00000120094
+ENSG00000122592
+ENSG00000125285
+ENSG00000125798
+ENSG00000125813
+ENSG00000125813
+ENSG00000125816
+ENSG00000125820
+ENSG00000128573
+ENSG00000128645
+ENSG00000128652
+ENSG00000128709
+ENSG00000128710
+ENSG00000128713
+ENSG00000128714
+ENSG00000129514
+ENSG00000131196
+ENSG00000131196
+ENSG00000136327
+ENSG00000136944
+ENSG00000138083
+ENSG00000139800
+ENSG00000143013
+ENSG00000143632
+ENSG00000144355
+ENSG00000148680
+ENSG00000148826
+ENSG00000151615
+ENSG00000152192
+ENSG00000152977
+ENSG00000159184
+ENSG00000159387
+ENSG00000163412
+ENSG00000163421
+ENSG00000163623
+ENSG00000164330
+ENSG00000164438
+ENSG00000164690
+ENSG00000164778
+ENSG00000165588
+ENSG00000165588
+ENSG00000165588
+ENSG00000166407
+ENSG00000166407
+ENSG00000168505
+ENSG00000168875
+ENSG00000169946
+ENSG00000170166
+ENSG00000170178
+ENSG00000170549
+ENSG00000170561
+ENSG00000170577
+ENSG00000170689
+ENSG00000173917
+ENSG00000174279
+ENSG00000174963
+ENSG00000174963
+ENSG00000175879
+ENSG00000176842
+ENSG00000177508
+ENSG00000178573
+ENSG00000182568
+ENSG00000182742
+ENSG00000185551
+ENSG00000185551
+ENSG00000187140
+ENSG00000196092
+ENSG00000197576
+ENSG00000198807
+ENSG00000253293
+ENSG00000256463
+ENSG00000260027
+ENSG00000276644
+ENSG00000285708

example_input_files/gene_classification/bivalent_promoters/lys4_only_gene_labels.txt ADDED Viewed

	@@ -0,0 +1,80 @@

+ENSG00000012048
+ENSG00000033627
+ENSG00000037042
+ENSG00000055950
+ENSG00000067596
+ENSG00000069248
+ENSG00000072682
+ENSG00000085274
+ENSG00000088035
+ENSG00000088930
+ENSG00000095539
+ENSG00000102471
+ENSG00000102967
+ENSG00000104313
+ENSG00000105146
+ENSG00000105379
+ENSG00000105982
+ENSG00000105983
+ENSG00000107816
+ENSG00000107819
+ENSG00000107829
+ENSG00000107833
+ENSG00000108784
+ENSG00000108799
+ENSG00000108828
+ENSG00000108830
+ENSG00000109911
+ENSG00000113522
+ENSG00000119487
+ENSG00000120049
+ENSG00000125347
+ENSG00000126581
+ENSG00000131374
+ENSG00000131437
+ENSG00000131462
+ENSG00000131467
+ENSG00000131469
+ENSG00000131470
+ENSG00000131475
+ENSG00000131477
+ENSG00000135272
+ENSG00000135776
+ENSG00000135801
+ENSG00000136158
+ENSG00000140262
+ENSG00000140450
+ENSG00000140563
+ENSG00000140829
+ENSG00000140830
+ENSG00000145494
+ENSG00000146909
+ENSG00000147905
+ENSG00000148688
+ENSG00000148840
+ENSG00000148950
+ENSG00000151332
+ENSG00000151338
+ENSG00000165637
+ENSG00000165644
+ENSG00000166135
+ENSG00000166136
+ENSG00000166167
+ENSG00000166169
+ENSG00000166189
+ENSG00000166197
+ENSG00000166377
+ENSG00000167081
+ENSG00000168118
+ENSG00000171421
+ENSG00000175832
+ENSG00000186480
+ENSG00000187098
+ENSG00000188554
+ENSG00000196628
+ENSG00000196628
+ENSG00000198728
+ENSG00000198728
+ENSG00000198863
+ENSG00000285283
+ENSG00000285708

example_input_files/gene_classification/bivalent_promoters/no_methylation_gene_labels.txt ADDED Viewed

	@@ -0,0 +1,42 @@

+ENSG00000068079
+ENSG00000068383
+ENSG00000075290
+ENSG00000104313
+ENSG00000105370
+ENSG00000105374
+ENSG00000105383
+ENSG00000106536
+ENSG00000113520
+ENSG00000113525
+ENSG00000118557
+ENSG00000125257
+ENSG00000128573
+ENSG00000131471
+ENSG00000131480
+ENSG00000131482
+ENSG00000134532
+ENSG00000136319
+ENSG00000138792
+ENSG00000140262
+ENSG00000140718
+ENSG00000147488
+ENSG00000147488
+ENSG00000148677
+ENSG00000151322
+ENSG00000151322
+ENSG00000156113
+ENSG00000164399
+ENSG00000164400
+ENSG00000167749
+ENSG00000167754
+ENSG00000167755
+ENSG00000169035
+ENSG00000170927
+ENSG00000182177
+ENSG00000186153
+ENSG00000187098
+ENSG00000204764
+ENSG00000213022
+ENSG00000213822
+ENSG00000261701
+ENSG00000285708

example_input_files/gene_classification/bivalent_promoters/panglao_SRA553822-SRS2119548.dataset/dataset.arrow ADDED Viewed

	@@ -0,0 +1,3 @@

+version https://git-lfs.github.com/spec/v1
+oid sha256:b12fd397c154a32257258e4946e784cc61808777400587a387fc15fd51bb331c
+size 56383064

example_input_files/gene_classification/bivalent_promoters/panglao_SRA553822-SRS2119548.dataset/dataset_info.json ADDED Viewed

	@@ -0,0 +1,3 @@

+version https://git-lfs.github.com/spec/v1
+oid sha256:ff9af262098e7ab85a3e2b73dfa371f77bce15b6f956f9c62509e72c5fba3b3e
+size 646

example_input_files/gene_classification/bivalent_promoters/panglao_SRA553822-SRS2119548.dataset/state.json ADDED Viewed

	@@ -0,0 +1,3 @@

+version https://git-lfs.github.com/spec/v1
+oid sha256:8b6551ec978a08f9da8c9461a4b73a272c68acccfb30503c5d79854369ccaef7
+size 383

example_input_files/gene_classification/dosage_sensitive_tfs/README.md ADDED Viewed

	@@ -0,0 +1 @@

+ The fine-tuning dataset for transcription factor dosage sensitivity application is 10,000 random cells from Genecorpus-30M. Please note that Genecorpus-30M is a large dataset so loading it for the first time may take some time. The Huggingface .dataset format is designed to cache the data though so future usage will be faster in that this cache allows Datasets to avoid re-processing the entire dataset with each use.

example_input_files/gene_classification/dosage_sensitive_tfs/dosage_sens_tf_labels.csv ADDED Viewed

	@@ -0,0 +1,369 @@

+dosage_sensitive,dosage_insensitive
+ENSG00000008197,ENSG00000010539
+ENSG00000008441,ENSG00000011590
+ENSG00000010818,ENSG00000063438
+ENSG00000011332,ENSG00000063587
+ENSG00000030419,ENSG00000064218
+ENSG00000062194,ENSG00000064489
+ENSG00000065970,ENSG00000067646
+ENSG00000067082,ENSG00000075407
+ENSG00000069667,ENSG00000079263
+ENSG00000072736,ENSG00000081386
+ENSG00000073282,ENSG00000083812
+ENSG00000073861,ENSG00000083814
+ENSG00000077092,ENSG00000083828
+ENSG00000083307,ENSG00000083838
+ENSG00000084676,ENSG00000083844
+ENSG00000085276,ENSG00000085644
+ENSG00000087510,ENSG00000089335
+ENSG00000087903,ENSG00000089775
+ENSG00000089225,ENSG00000102901
+ENSG00000091656,ENSG00000103199
+ENSG00000091831,ENSG00000105136
+ENSG00000095951,ENSG00000105610
+ENSG00000100644,ENSG00000105672
+ENSG00000100968,ENSG00000106410
+ENSG00000101076,ENSG00000106948
+ENSG00000101412,ENSG00000109705
+ENSG00000102870,ENSG00000115568
+ENSG00000102935,ENSG00000117010
+ENSG00000103449,ENSG00000118620
+ENSG00000105698,ENSG00000119574
+ENSG00000105866,ENSG00000120669
+ENSG00000106689,ENSG00000121406
+ENSG00000106852,ENSG00000121864
+ENSG00000111249,ENSG00000122085
+ENSG00000111783,ENSG00000124203
+ENSG00000112033,ENSG00000124232
+ENSG00000112246,ENSG00000124444
+ENSG00000112561,ENSG00000124613
+ENSG00000112837,ENSG00000125520
+ENSG00000115112,ENSG00000127081
+ENSG00000116809,ENSG00000127903
+ENSG00000116833,ENSG00000127989
+ENSG00000117000,ENSG00000129028
+ENSG00000118263,ENSG00000129071
+ENSG00000118922,ENSG00000129194
+ENSG00000119547,ENSG00000130544
+ENSG00000120798,ENSG00000130818
+ENSG00000121068,ENSG00000131848
+ENSG00000123358,ENSG00000132010
+ENSG00000123411,ENSG00000132846
+ENSG00000124496,ENSG00000133250
+ENSG00000124813,ENSG00000134874
+ENSG00000125398,ENSG00000135899
+ENSG00000125618,ENSG00000136866
+ENSG00000126368,ENSG00000137185
+ENSG00000127152,ENSG00000137504
+ENSG00000128573,ENSG00000138380
+ENSG00000129173,ENSG00000140993
+ENSG00000131759,ENSG00000141946
+ENSG00000132005,ENSG00000142556
+ENSG00000133794,ENSG00000143067
+ENSG00000134046,ENSG00000144026
+ENSG00000134317,ENSG00000144161
+ENSG00000134323,ENSG00000145908
+ENSG00000134852,ENSG00000146587
+ENSG00000135111,ENSG00000147183
+ENSG00000137203,ENSG00000147789
+ENSG00000137270,ENSG00000148300
+ENSG00000138795,ENSG00000149054
+ENSG00000139083,ENSG00000149922
+ENSG00000139793,ENSG00000151500
+ENSG00000140548,ENSG00000151650
+ENSG00000140968,ENSG00000151657
+ENSG00000142611,ENSG00000152439
+ENSG00000143033,ENSG00000152467
+ENSG00000143171,ENSG00000152475
+ENSG00000143190,ENSG00000153975
+ENSG00000143355,ENSG00000155592
+ENSG00000143365,ENSG00000156469
+ENSG00000143373,ENSG00000157429
+ENSG00000143437,ENSG00000159882
+ENSG00000144355,ENSG00000159885
+ENSG00000147862,ENSG00000159915
+ENSG00000148516,ENSG00000160224
+ENSG00000150907,ENSG00000160229
+ENSG00000151090,ENSG00000160352
+ENSG00000153234,ENSG00000160908
+ENSG00000158055,ENSG00000160961
+ENSG00000160007,ENSG00000161277
+ENSG00000160094,ENSG00000162086
+ENSG00000161405,ENSG00000163516
+ENSG00000162761,ENSG00000164011
+ENSG00000162924,ENSG00000164048
+ENSG00000164683,ENSG00000164296
+ENSG00000164684,ENSG00000164299
+ENSG00000167182,ENSG00000165066
+ENSG00000168610,ENSG00000165512
+ENSG00000168916,ENSG00000165643
+ENSG00000169554,ENSG00000165684
+ENSG00000169946,ENSG00000166529
+ENSG00000170370,ENSG00000166823
+ENSG00000172733,ENSG00000166860
+ENSG00000172819,ENSG00000167034
+ENSG00000177463,ENSG00000167384
+ENSG00000178177,ENSG00000167554
+ENSG00000179348,ENSG00000167625
+ENSG00000179361,ENSG00000167785
+ENSG00000179456,ENSG00000167800
+ENSG00000180357,ENSG00000167840
+ENSG00000185551,ENSG00000167962
+ENSG00000185591,ENSG00000167981
+ENSG00000187098,ENSG00000168152
+ENSG00000187605,ENSG00000168286
+ENSG00000189308,ENSG00000168769
+ENSG00000196092,ENSG00000169131
+ENSG00000196482,ENSG00000169136
+ENSG00000196628,ENSG00000169548
+ENSG00000197757,ENSG00000169951
+ENSG00000198815,ENSG00000169955
+ENSG00000198945,ENSG00000169989
+ENSG00000198963,ENSG00000170260
+ENSG00000204231,ENSG00000170608
+,ENSG00000170954
+,ENSG00000171291
+,ENSG00000171295
+,ENSG00000171425
+,ENSG00000171443
+,ENSG00000171466
+,ENSG00000171469
+,ENSG00000171574
+,ENSG00000171606
+,ENSG00000171827
+,ENSG00000171872
+,ENSG00000171970
+,ENSG00000172000
+,ENSG00000172888
+,ENSG00000173041
+,ENSG00000173258
+,ENSG00000173480
+,ENSG00000173673
+,ENSG00000173825
+,ENSG00000174255
+,ENSG00000174652
+,ENSG00000174796
+,ENSG00000175279
+,ENSG00000175325
+,ENSG00000175395
+,ENSG00000175691
+,ENSG00000176009
+,ENSG00000176024
+,ENSG00000176083
+,ENSG00000176222
+,ENSG00000176302
+,ENSG00000176472
+,ENSG00000176678
+,ENSG00000176679
+,ENSG00000177030
+,ENSG00000177494
+,ENSG00000177599
+,ENSG00000177683
+,ENSG00000177842
+,ENSG00000177873
+,ENSG00000177932
+,ENSG00000177946
+,ENSG00000178150
+,ENSG00000178229
+,ENSG00000178338
+,ENSG00000178386
+,ENSG00000178665
+,ENSG00000178917
+,ENSG00000178928
+,ENSG00000178935
+,ENSG00000179195
+,ENSG00000179772
+,ENSG00000179774
+,ENSG00000179886
+,ENSG00000179909
+,ENSG00000179922
+,ENSG00000179930
+,ENSG00000179943
+,ENSG00000179965
+,ENSG00000180257
+,ENSG00000180346
+,ENSG00000180532
+,ENSG00000180535
+,ENSG00000180938
+,ENSG00000181135
+,ENSG00000181444
+,ENSG00000181450
+,ENSG00000181638
+,ENSG00000181894
+,ENSG00000181896
+,ENSG00000182318
+,ENSG00000182983
+,ENSG00000182986
+,ENSG00000183340
+,ENSG00000183647
+,ENSG00000183734
+,ENSG00000183850
+,ENSG00000184221
+,ENSG00000184517
+,ENSG00000184635
+,ENSG00000184677
+,ENSG00000184895
+,ENSG00000185155
+,ENSG00000185252
+,ENSG00000185404
+,ENSG00000185730
+,ENSG00000186020
+,ENSG00000186026
+,ENSG00000186051
+,ENSG00000186103
+,ENSG00000186230
+,ENSG00000186300
+,ENSG00000186376
+,ENSG00000186446
+,ENSG00000186496
+,ENSG00000186777
+,ENSG00000186812
+,ENSG00000186814
+,ENSG00000187626
+,ENSG00000187801
+,ENSG00000187821
+,ENSG00000187855
+,ENSG00000187987
+,ENSG00000188033
+,ENSG00000188095
+,ENSG00000188171
+,ENSG00000188295
+,ENSG00000188321
+,ENSG00000188629
+,ENSG00000188785
+,ENSG00000188868
+,ENSG00000189164
+,ENSG00000189190
+,ENSG00000189298
+,ENSG00000189299
+,ENSG00000196152
+,ENSG00000196172
+,ENSG00000196214
+,ENSG00000196345
+,ENSG00000196357
+,ENSG00000196378
+,ENSG00000196381
+,ENSG00000196387
+,ENSG00000196391
+,ENSG00000196417
+,ENSG00000196418
+,ENSG00000196456
+,ENSG00000196460
+,ENSG00000196466
+,ENSG00000196605
+,ENSG00000196646
+,ENSG00000196652
+,ENSG00000196670
+,ENSG00000196693
+,ENSG00000196705
+,ENSG00000196812
+,ENSG00000196946
+,ENSG00000197008
+,ENSG00000197020
+,ENSG00000197037
+,ENSG00000197044
+,ENSG00000197054
+,ENSG00000197124
+,ENSG00000197134
+,ENSG00000197162
+,ENSG00000197213
+,ENSG00000197279
+,ENSG00000197343
+,ENSG00000197360
+,ENSG00000197363
+,ENSG00000197472
+,ENSG00000197779
+,ENSG00000197841
+,ENSG00000197857
+,ENSG00000197863
+,ENSG00000197928
+,ENSG00000197933
+,ENSG00000197951
+,ENSG00000198028
+,ENSG00000198039
+,ENSG00000198046
+,ENSG00000198185
+,ENSG00000198205
+,ENSG00000198300
+,ENSG00000198315
+,ENSG00000198342
+,ENSG00000198346
+,ENSG00000198429
+,ENSG00000198440
+,ENSG00000198464
+,ENSG00000198466
+,ENSG00000198482
+,ENSG00000198538
+,ENSG00000198546
+,ENSG00000198551
+,ENSG00000198556
+,ENSG00000198633
+,ENSG00000198939
+,ENSG00000203326
+,ENSG00000204514
+,ENSG00000204519
+,ENSG00000204532
+,ENSG00000204595
+,ENSG00000204604
+,ENSG00000204644
+,ENSG00000204946
+,ENSG00000213020
+,ENSG00000213799
+,ENSG00000213973
+,ENSG00000213988
+,ENSG00000214189
+,ENSG00000215271
+,ENSG00000215372
+,ENSG00000215612
+,ENSG00000220201
+,ENSG00000221923
+,ENSG00000223547
+,ENSG00000227124
+,ENSG00000229676
+,ENSG00000229809
+,ENSG00000230797
+,ENSG00000232040
+,ENSG00000234284
+,ENSG00000234444
+,ENSG00000235109
+,ENSG00000235608
+,ENSG00000236104
+,ENSG00000236609
+,ENSG00000237440
+,ENSG00000242852
+,ENSG00000243660
+,ENSG00000245680
+,ENSG00000248483
+,ENSG00000249459
+,ENSG00000249471
+,ENSG00000249709
+,ENSG00000250571
+,ENSG00000250709
+,ENSG00000251192
+,ENSG00000251247
+,ENSG00000251369
+,ENSG00000253831
+,ENSG00000254004
+,ENSG00000256087
+,ENSG00000256223
+,ENSG00000256229
+,ENSG00000256294
+,ENSG00000256463
+,ENSG00000256683
+,ENSG00000256771
+,ENSG00000257446
+,ENSG00000257591
+,ENSG00000258405
+,ENSG00000258873
+,ENSG00000263002
+,ENSG00000264668
+,ENSG00000265763
+,ENSG00000267041
+,ENSG00000267179
+,ENSG00000267281
+,ENSG00000267508
+,ENSG00000267680
+,ENSG00000269067
+,ENSG00000269343
+,ENSG00000269699
+,ENSG00000272602

example_input_files/gene_info_table.csv ADDED Viewed

The diff for this file is too large to render. See raw diff