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Datasets:
scShape-Benchmark
/
scShapeBench

Tasks:
Tabular Classification
Tabular Regression
Size:
1M<n<10M
Tags:
single-cell
rna-seq
scRNA-seq
h5ad
anndata
genomics
License:
Dataset card Files
xet
Joao Felipe Rocha Claude Sonnet 4.6 commited on
Commit
f4f05c5
·
1 Parent(s): 850fd82

Add data/sample/ config with 9 representative h5ad files for reviewers

Browse files

Adds a new 'sample' dataset config (~2.6 GB) containing 9 files spanning
small/medium/large cell-count tiers, so reviewers can inspect data quality
without downloading the full 116 GB scRNAseq corpus. Also fixes dataset_index.csv
filename paths to include the scRNAseq/ directory prefix.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Files changed (11) hide show
  1. README.md +29 -0
  2. data/sample/SCD-0002.h5ad +3 -0
  3. data/sample/SCD-0006.h5ad +3 -0
  4. data/sample/SCD-0010.h5ad +3 -0
  5. data/sample/SCD-0014.h5ad +3 -0
  6. data/sample/SCD-0015.h5ad +3 -0
  7. data/sample/SCD-0052.h5ad +3 -0
  8. data/sample/SCD-0062.h5ad +3 -0
  9. data/sample/SCD-0071.h5ad +3 -0
  10. data/sample/SCD-0074.h5ad +3 -0
  11. dataset_index.csv +105 -105
README.md CHANGED
@@ -21,6 +21,10 @@ configs:
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  data_files:
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  - split: train
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  path: data/scRNAseq/*.h5ad
 
 
 
 
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  - config_name: synthetic
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  data_files:
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  - split: train
@@ -187,6 +191,31 @@ majority = labels[labels["aggregation"] == "majority"].set_index("dataset_id")
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  union = labels[labels["aggregation"] == "union"].set_index("dataset_id")
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  ```
189
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  ## Croissant Metadata
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  This dataset includes a `croissant.json` file conforming to the [Croissant 1.1](https://docs.mlcommons.org/croissant/) metadata standard. This enables programmatic discovery and loading of dataset metadata through compatible tools.
 
21
  data_files:
22
  - split: train
23
  path: data/scRNAseq/*.h5ad
24
+ - config_name: sample
25
+ data_files:
26
+ - split: train
27
+ path: data/sample/*.h5ad
28
  - config_name: synthetic
29
  data_files:
30
  - split: train
 
191
  union = labels[labels["aggregation"] == "union"].set_index("dataset_id")
192
  ```
193
 
194
+ ## Sample Data
195
+
196
+ The full scRNAseq configuration is ~116 GB. A representative sample (~2.6 GB) is available at [`data/sample/`](data/sample/) and accessible as the `sample` config:
197
+
198
+ ```python
199
+ from datasets import load_dataset
200
+ ds = load_dataset("scShape-Benchmark/scShapeBench", "sample")
201
+ ```
202
+
203
+ It contains **9 `.h5ad` files** selected to span the range of dataset sizes present in the full benchmark:
204
+
205
+ | File | Cells | Size |
206
+ |------|------:|-----:|
207
+ | `SCD-0006.h5ad` | 1,163 | 61 MB |
208
+ | `SCD-0014.h5ad` | 1,886 | 57 MB |
209
+ | `SCD-0015.h5ad` | 1,973 | 57 MB |
210
+ | `SCD-0010.h5ad` | 8,686 | 56 MB |
211
+ | `SCD-0002.h5ad` | 8,368 | 227 MB |
212
+ | `SCD-0052.h5ad` | 9,669 | 211 MB |
213
+ | `SCD-0062.h5ad` | 7,976 | 223 MB |
214
+ | `SCD-0071.h5ad` | 18,890 | 858 MB |
215
+ | `SCD-0074.h5ad` | 21,225 | 823 MB |
216
+
217
+ **Selection criteria:** Files were chosen to cover three size tiers — small (<80 MB, 4 files), medium (200–230 MB, 3 files), and large (>800 MB, 2 files) — so reviewers can inspect data at each scale without downloading the full corpus. Within each tier, files were selected by ascending file size from the full `dataset_index.csv`. All lightweight metadata files (`labels/`, `dataset_index.csv`, `cell_metadata.csv`, `gene_metadata.csv`) are available in full regardless of which scRNAseq files are downloaded.
218
+
219
  ## Croissant Metadata
220
 
221
  This dataset includes a `croissant.json` file conforming to the [Croissant 1.1](https://docs.mlcommons.org/croissant/) metadata standard. This enables programmatic discovery and loading of dataset metadata through compatible tools.
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data/sample/SCD-0052.h5ad ADDED
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data/sample/SCD-0062.h5ad ADDED
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data/sample/SCD-0071.h5ad ADDED
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dataset_index.csv CHANGED
@@ -1,106 +1,106 @@
1
  file_id,filename,n_cells,n_genes,file_size_bytes
2
- SCD-0001,SCD-0001.h5ad,12287,28385,327524590
3
- SCD-0002,SCD-0002.h5ad,8368,21048,226775880
4
- SCD-0003,SCD-0003.h5ad,12279,24197,394231074
5
- SCD-0004,SCD-0004.h5ad,12735,47839,629714512
6
- SCD-0005,SCD-0005.h5ad,13784,46154,567821390
7
- SCD-0006,SCD-0006.h5ad,1163,22238,61085856
8
- SCD-0007,SCD-0007.h5ad,6382,19545,121612805
9
- SCD-0008,SCD-0008.h5ad,5218,45802,282100584
10
- SCD-0009,SCD-0009.h5ad,6082,42208,267173682
11
- SCD-0010,SCD-0010.h5ad,8686,16028,56249682
12
- SCD-0011,SCD-0011.h5ad,16956,17354,199605298
13
- SCD-0012,SCD-0012.h5ad,4286,18354,105686732
14
- SCD-0013,SCD-0013.h5ad,49205,28344,1685440653
15
- SCD-0014,SCD-0014.h5ad,1886,15599,57297523
16
- SCD-0015,SCD-0015.h5ad,1973,18961,57332812
17
- SCD-0016,SCD-0016.h5ad,19113,14984,605030177
18
- SCD-0017,SCD-0017.h5ad,18225,14446,435124269
19
- SCD-0018,SCD-0018.h5ad,9596,26313,243405375
20
- SCD-0019,SCD-0019.h5ad,4570,18725,118200629
21
- SCD-0020,SCD-0020.h5ad,5662,25552,157222918
22
- SCD-0021,SCD-0021.h5ad,4744,23103,137277281
23
- SCD-0022,SCD-0022.h5ad,5958,24216,174928774
24
- SCD-0023,SCD-0023.h5ad,5697,25348,171094413
25
- SCD-0024,SCD-0024.h5ad,13838,25395,382428699
26
- SCD-0025,SCD-0025.h5ad,12512,27763,401852301
27
- SCD-0026,SCD-0026.h5ad,8958,14261,268992816
28
- SCD-0027,SCD-0027.h5ad,15440,28630,493817980
29
- SCD-0028,SCD-0028.h5ad,20079,14593,449986038
30
- SCD-0029,SCD-0029.h5ad,19892,14345,276497563
31
- SCD-0030,SCD-0030.h5ad,5045,25273,137446455
32
- SCD-0033,SCD-0033.h5ad,49995,33039,13258967478
33
- SCD-0037,SCD-0037.h5ad,434340,41625,13459646409
34
- SCD-0038,SCD-0038.h5ad,3785,4210,70302927
35
- SCD-0039,SCD-0039.h5ad,91064,29540,1388886240
36
- SCD-0040,SCD-0040.h5ad,4688,31053,69293553
37
- SCD-0041,SCD-0041.h5ad,273885,53801,9087347191
38
- SCD-0042,SCD-0042.h5ad,22048,34010,291844987
39
- SCD-0045,SCD-0045.h5ad,40220,17943,573889475
40
- SCD-0046,SCD-0046.h5ad,35718,17943,424796295
41
- SCD-0047,SCD-0047.h5ad,24540,17943,302266876
42
- SCD-0048,SCD-0048.h5ad,24540,17943,302266876
43
- SCD-0049,SCD-0049.h5ad,21647,17943,343537430
44
- SCD-0050,SCD-0050.h5ad,20680,17943,463061707
45
- SCD-0051,SCD-0051.h5ad,12295,17943,179006530
46
- SCD-0052,SCD-0052.h5ad,9669,21025,211220918
47
- SCD-0053,SCD-0053.h5ad,9275,17943,131391459
48
- SCD-0054,SCD-0054.h5ad,8945,17943,190200759
49
- SCD-0055,SCD-0055.h5ad,8311,21025,266084901
50
- SCD-0056,SCD-0056.h5ad,7976,17943,105259943
51
- SCD-0057,SCD-0057.h5ad,7294,17943,134521743
52
- SCD-0058,SCD-0058.h5ad,6777,17943,126168147
53
- SCD-0059,SCD-0059.h5ad,6201,17943,68968282
54
- SCD-0060,SCD-0060.h5ad,4047,21025,76112546
55
- SCD-0061,SCD-0061.h5ad,8945,17943,190200759
56
- SCD-0062,SCD-0062.h5ad,7976,17984,222683560
57
- SCD-0063,SCD-0063.h5ad,7294,17984,286782960
58
- SCD-0064,SCD-0064.h5ad,6777,17984,266800552
59
- SCD-0065,SCD-0065.h5ad,6201,17984,147681520
60
- SCD-0066,SCD-0066.h5ad,4047,21069,140290523
61
- SCD-0067,SCD-0067.h5ad,8945,17984,402683352
62
- SCD-0068,SCD-0068.h5ad,31586,458,68445964
63
- SCD-0069,SCD-0069.h5ad,19601,29067,606799733
64
- SCD-0070,SCD-0070.h5ad,24489,29067,1093943669
65
- SCD-0071,SCD-0071.h5ad,18890,61427,857636781
66
- SCD-0072,SCD-0072.h5ad,20727,33105,363850352
67
- SCD-0073,SCD-0073.h5ad,25908,32787,472576593
68
- SCD-0074,SCD-0074.h5ad,21225,36406,823047104
69
- SCD-0075,SCD-0075.h5ad,22227,36406,894501029
70
- SCD-0076,SCD-0076.h5ad,19317,33137,566581757
71
- SCD-0077,SCD-0077.h5ad,20611,33137,651703937
72
- SCD-0078,SCD-0078.h5ad,25382,34455,459764974
73
- SCD-0079,SCD-0079.h5ad,20916,26570,654252626
74
- SCD-0080,SCD-0080.h5ad,20556,28748,3777273280
75
- SCD-0081,SCD-0081.h5ad,27589,32839,1576722250
76
- SCD-0082,SCD-0082.h5ad,18524,32839,908133613
77
- SCD-0083,SCD-0083.h5ad,20321,33137,449160253
78
- SCD-0084,SCD-0084.h5ad,26129,36412,3000296958
79
- SCD-0085,SCD-0085.h5ad,28758,22214,1174768556
80
- SCD-0086,SCD-0086.h5ad,17706,32839,558642395
81
- SCD-0087,SCD-0087.h5ad,22891,36412,2176410370
82
- SCD-0088,SCD-0088.h5ad,21443,36412,1853731314
83
- SCD-0089,SCD-0089.h5ad,24025,31815,605943519
84
- SCD-0090,SCD-0090.h5ad,18011,30867,2883826588
85
- SCD-0091,SCD-0091.h5ad,22125,32787,501820095
86
- SCD-0092,SCD-0092.h5ad,24342,61427,784760173
87
- SCD-0093,SCD-0093.h5ad,21422,30867,3026551729
88
- SCD-0094,SCD-0094.h5ad,19711,18786,2979892533
89
- SCD-0095,SCD-0095.h5ad,19037,27299,530025067
90
- SCD-0096,SCD-0096.h5ad,24792,36412,1882648572
91
- SCD-0097,SCD-0097.h5ad,22168,36412,1533509796
92
- SCD-0098,SCD-0098.h5ad,24081,33091,750829667
93
- SCD-0099,SCD-0099.h5ad,28943,18786,4079740221
94
- SCD-0100,SCD-0100.h5ad,22214,61759,2106410949
95
- SCD-0101,SCD-0101.h5ad,21030,61759,2272576373
96
- SCD-0102,SCD-0102.h5ad,17786,61759,1484522113
97
- SCD-0103,SCD-0103.h5ad,22671,61759,2451822346
98
- SCD-0104,SCD-0104.h5ad,22029,61759,2268820176
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- SCD-0105,SCD-0105.h5ad,28718,18786,3976948680
100
- SCD-0106,SCD-0106.h5ad,26853,23083,1528787178
101
- SCD-0107,SCD-0107.h5ad,27665,36406,1215848784
102
- SCD-0108,SCD-0108.h5ad,26601,37002,1295574123
103
- SCD-0109,SCD-0109.h5ad,26935,37002,1009547690
104
- SCD-0110,SCD-0110.h5ad,20779,36406,245421969
105
- SCD-0111,SCD-0111.h5ad,25726,36406,456409190
106
- SCD-0112,SCD-0112.h5ad,26313,36406,314443323
 
1
  file_id,filename,n_cells,n_genes,file_size_bytes
2
+ SCD-0001,scRNAseq/SCD-0001.h5ad,12287,28385,327524590
3
+ SCD-0002,scRNAseq/SCD-0002.h5ad,8368,21048,226775880
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+ SCD-0003,scRNAseq/SCD-0003.h5ad,12279,24197,394231074
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+ SCD-0004,scRNAseq/SCD-0004.h5ad,12735,47839,629714512
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+ SCD-0005,scRNAseq/SCD-0005.h5ad,13784,46154,567821390
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+ SCD-0006,scRNAseq/SCD-0006.h5ad,1163,22238,61085856
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+ SCD-0007,scRNAseq/SCD-0007.h5ad,6382,19545,121612805
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+ SCD-0008,scRNAseq/SCD-0008.h5ad,5218,45802,282100584
10
+ SCD-0009,scRNAseq/SCD-0009.h5ad,6082,42208,267173682
11
+ SCD-0010,scRNAseq/SCD-0010.h5ad,8686,16028,56249682
12
+ SCD-0011,scRNAseq/SCD-0011.h5ad,16956,17354,199605298
13
+ SCD-0012,scRNAseq/SCD-0012.h5ad,4286,18354,105686732
14
+ SCD-0013,scRNAseq/SCD-0013.h5ad,49205,28344,1685440653
15
+ SCD-0014,scRNAseq/SCD-0014.h5ad,1886,15599,57297523
16
+ SCD-0015,scRNAseq/SCD-0015.h5ad,1973,18961,57332812
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+ SCD-0016,scRNAseq/SCD-0016.h5ad,19113,14984,605030177
18
+ SCD-0017,scRNAseq/SCD-0017.h5ad,18225,14446,435124269
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+ SCD-0018,scRNAseq/SCD-0018.h5ad,9596,26313,243405375
20
+ SCD-0019,scRNAseq/SCD-0019.h5ad,4570,18725,118200629
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+ SCD-0020,scRNAseq/SCD-0020.h5ad,5662,25552,157222918
22
+ SCD-0021,scRNAseq/SCD-0021.h5ad,4744,23103,137277281
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+ SCD-0022,scRNAseq/SCD-0022.h5ad,5958,24216,174928774
24
+ SCD-0023,scRNAseq/SCD-0023.h5ad,5697,25348,171094413
25
+ SCD-0024,scRNAseq/SCD-0024.h5ad,13838,25395,382428699
26
+ SCD-0025,scRNAseq/SCD-0025.h5ad,12512,27763,401852301
27
+ SCD-0026,scRNAseq/SCD-0026.h5ad,8958,14261,268992816
28
+ SCD-0027,scRNAseq/SCD-0027.h5ad,15440,28630,493817980
29
+ SCD-0028,scRNAseq/SCD-0028.h5ad,20079,14593,449986038
30
+ SCD-0029,scRNAseq/SCD-0029.h5ad,19892,14345,276497563
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+ SCD-0030,scRNAseq/SCD-0030.h5ad,5045,25273,137446455
32
+ SCD-0033,scRNAseq/SCD-0033.h5ad,49995,33039,13258967478
33
+ SCD-0037,scRNAseq/SCD-0037.h5ad,434340,41625,13459646409
34
+ SCD-0038,scRNAseq/SCD-0038.h5ad,3785,4210,70302927
35
+ SCD-0039,scRNAseq/SCD-0039.h5ad,91064,29540,1388886240
36
+ SCD-0040,scRNAseq/SCD-0040.h5ad,4688,31053,69293553
37
+ SCD-0041,scRNAseq/SCD-0041.h5ad,273885,53801,9087347191
38
+ SCD-0042,scRNAseq/SCD-0042.h5ad,22048,34010,291844987
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+ SCD-0045,scRNAseq/SCD-0045.h5ad,40220,17943,573889475
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+ SCD-0046,scRNAseq/SCD-0046.h5ad,35718,17943,424796295
41
+ SCD-0047,scRNAseq/SCD-0047.h5ad,24540,17943,302266876
42
+ SCD-0048,scRNAseq/SCD-0048.h5ad,24540,17943,302266876
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+ SCD-0049,scRNAseq/SCD-0049.h5ad,21647,17943,343537430
44
+ SCD-0050,scRNAseq/SCD-0050.h5ad,20680,17943,463061707
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+ SCD-0051,scRNAseq/SCD-0051.h5ad,12295,17943,179006530
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+ SCD-0052,scRNAseq/SCD-0052.h5ad,9669,21025,211220918
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+ SCD-0053,scRNAseq/SCD-0053.h5ad,9275,17943,131391459
48
+ SCD-0054,scRNAseq/SCD-0054.h5ad,8945,17943,190200759
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+ SCD-0055,scRNAseq/SCD-0055.h5ad,8311,21025,266084901
50
+ SCD-0056,scRNAseq/SCD-0056.h5ad,7976,17943,105259943
51
+ SCD-0057,scRNAseq/SCD-0057.h5ad,7294,17943,134521743
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+ SCD-0058,scRNAseq/SCD-0058.h5ad,6777,17943,126168147
53
+ SCD-0059,scRNAseq/SCD-0059.h5ad,6201,17943,68968282
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+ SCD-0060,scRNAseq/SCD-0060.h5ad,4047,21025,76112546
55
+ SCD-0061,scRNAseq/SCD-0061.h5ad,8945,17943,190200759
56
+ SCD-0062,scRNAseq/SCD-0062.h5ad,7976,17984,222683560
57
+ SCD-0063,scRNAseq/SCD-0063.h5ad,7294,17984,286782960
58
+ SCD-0064,scRNAseq/SCD-0064.h5ad,6777,17984,266800552
59
+ SCD-0065,scRNAseq/SCD-0065.h5ad,6201,17984,147681520
60
+ SCD-0066,scRNAseq/SCD-0066.h5ad,4047,21069,140290523
61
+ SCD-0067,scRNAseq/SCD-0067.h5ad,8945,17984,402683352
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+ SCD-0068,scRNAseq/SCD-0068.h5ad,31586,458,68445964
63
+ SCD-0069,scRNAseq/SCD-0069.h5ad,19601,29067,606799733
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+ SCD-0070,scRNAseq/SCD-0070.h5ad,24489,29067,1093943669
65
+ SCD-0071,scRNAseq/SCD-0071.h5ad,18890,61427,857636781
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+ SCD-0072,scRNAseq/SCD-0072.h5ad,20727,33105,363850352
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+ SCD-0073,scRNAseq/SCD-0073.h5ad,25908,32787,472576593
68
+ SCD-0074,scRNAseq/SCD-0074.h5ad,21225,36406,823047104
69
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70
+ SCD-0076,scRNAseq/SCD-0076.h5ad,19317,33137,566581757
71
+ SCD-0077,scRNAseq/SCD-0077.h5ad,20611,33137,651703937
72
+ SCD-0078,scRNAseq/SCD-0078.h5ad,25382,34455,459764974
73
+ SCD-0079,scRNAseq/SCD-0079.h5ad,20916,26570,654252626
74
+ SCD-0080,scRNAseq/SCD-0080.h5ad,20556,28748,3777273280
75
+ SCD-0081,scRNAseq/SCD-0081.h5ad,27589,32839,1576722250
76
+ SCD-0082,scRNAseq/SCD-0082.h5ad,18524,32839,908133613
77
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78
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79
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80
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81
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82
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84
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85
+ SCD-0091,scRNAseq/SCD-0091.h5ad,22125,32787,501820095
86
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87
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88
+ SCD-0094,scRNAseq/SCD-0094.h5ad,19711,18786,2979892533
89
+ SCD-0095,scRNAseq/SCD-0095.h5ad,19037,27299,530025067
90
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91
+ SCD-0097,scRNAseq/SCD-0097.h5ad,22168,36412,1533509796
92
+ SCD-0098,scRNAseq/SCD-0098.h5ad,24081,33091,750829667
93
+ SCD-0099,scRNAseq/SCD-0099.h5ad,28943,18786,4079740221
94
+ SCD-0100,scRNAseq/SCD-0100.h5ad,22214,61759,2106410949
95
+ SCD-0101,scRNAseq/SCD-0101.h5ad,21030,61759,2272576373
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+ SCD-0102,scRNAseq/SCD-0102.h5ad,17786,61759,1484522113
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+ SCD-0103,scRNAseq/SCD-0103.h5ad,22671,61759,2451822346
98
+ SCD-0104,scRNAseq/SCD-0104.h5ad,22029,61759,2268820176
99
+ SCD-0105,scRNAseq/SCD-0105.h5ad,28718,18786,3976948680
100
+ SCD-0106,scRNAseq/SCD-0106.h5ad,26853,23083,1528787178
101
+ SCD-0107,scRNAseq/SCD-0107.h5ad,27665,36406,1215848784
102
+ SCD-0108,scRNAseq/SCD-0108.h5ad,26601,37002,1295574123
103
+ SCD-0109,scRNAseq/SCD-0109.h5ad,26935,37002,1009547690
104
+ SCD-0110,scRNAseq/SCD-0110.h5ad,20779,36406,245421969
105
+ SCD-0111,scRNAseq/SCD-0111.h5ad,25726,36406,456409190
106
+ SCD-0112,scRNAseq/SCD-0112.h5ad,26313,36406,314443323