Datasets:

Boom5426
/

PertResolve_Bench

Error code:   DatasetGenerationCastError
Exception:    DatasetGenerationCastError
Message:      An error occurred while generating the dataset

All the data files must have the same columns, but at some point there are 7 new columns ({'prolif_z', 'facs_z', 'cell', 'cluster', 'diffusion', 'consequence', 'GT'}) and 20 missing columns ({'fold_core', 'is_hotspot', 'clinvar_pathogenic', 'aa_changes', 'cat_switch', 'severity_dist', 'n_aa_changes', 'd_hydro', 'in_holdout1', 'positions', 'primary_position', 'n_cells', 'in_holdout4', 'd_charge', 'in_holdout3', 'd_vol', 'in_holdout2', 'is_wt', 'mutation_name', 'in_holdout5'}).

This happened while the csv dataset builder was generating data using

hf://datasets/Boom5426/PertResolve_Bench/allele/jak1/jak1_cell_metadata.csv (at revision 132febe114b2593c9671c73a862fd0abd3d2f855), ['hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/gata1/gata1_theta.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/gata1/gata1_variants.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/jak1/jak1_cell_metadata.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/jak1/jak1_gene_info.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/jak1/jak1_theta.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/jak1/metadata_genotyped_experiment.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_KRAS.processed.cells.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_KRAS.processed.cells.metadata.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_KRAS.processed.genes.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_KRAS.variants2cell.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_TP53.processed.cells.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_TP53.processed.cells.metadata.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_TP53.processed.genes.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_TP53.variants2cell.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/benchmark/allele_perturb_bench.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/external/scperturb/manifest.tsv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/external/vcc/gene_names.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/external/vcc/pert_counts_Validation.csv']

Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback:    Traceback (most recent call last):
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1848, in _prepare_split_single
                  writer.write_table(table)
                  ~~~~~~~~~~~~~~~~~~^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 765, in write_table
                  self._write_table(pa_table, writer_batch_size=writer_batch_size)
                  ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 773, in _write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2378, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2306, in cast_table_to_schema
                  raise CastError(
                  ...<3 lines>...
                  )
              datasets.table.CastError: Couldn't cast
              cell: string
              GT: string
              consequence: string
              cluster: string
              facs_z: double
              prolif_z: double
              diffusion: double
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1077
              to
              {'mutation_name': Value('string'), 'n_cells': Value('int64'), 'is_wt': Value('bool'), 'n_aa_changes': Value('int64'), 'aa_changes': Value('string'), 'positions': Value('string'), 'primary_position': Value('int64'), 'in_holdout1': Value('bool'), 'in_holdout2': Value('bool'), 'in_holdout3': Value('bool'), 'in_holdout4': Value('bool'), 'in_holdout5': Value('bool'), 'd_hydro': Value('float64'), 'd_vol': Value('float64'), 'd_charge': Value('float64'), 'fold_core': Value('float64'), 'cat_switch': Value('float64'), 'is_hotspot': Value('float64'), 'severity_dist': Value('float64'), 'clinvar_pathogenic': Value('float64')}
              because column names don't match
              
              During handling of the above exception, another exception occurred:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1369, in compute_config_parquet_and_info_response
                  parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
                                                                        ~~~~~~~~~~~~~~~~~~~~~~~~~^
                      builder, max_dataset_size_bytes=max_dataset_size_bytes
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  )
                  ^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
                  builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
                  ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1694, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                                               ~~~~~~~~~~~~~~~~~~~~~~~~~~^
                      gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  ):
                  ^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1850, in _prepare_split_single
                  raise DatasetGenerationCastError.from_cast_error(
                  ...<4 lines>...
                  )
              datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
              
              All the data files must have the same columns, but at some point there are 7 new columns ({'prolif_z', 'facs_z', 'cell', 'cluster', 'diffusion', 'consequence', 'GT'}) and 20 missing columns ({'fold_core', 'is_hotspot', 'clinvar_pathogenic', 'aa_changes', 'cat_switch', 'severity_dist', 'n_aa_changes', 'd_hydro', 'in_holdout1', 'positions', 'primary_position', 'n_cells', 'in_holdout4', 'd_charge', 'in_holdout3', 'd_vol', 'in_holdout2', 'is_wt', 'mutation_name', 'in_holdout5'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/Boom5426/PertResolve_Bench/allele/jak1/jak1_cell_metadata.csv (at revision 132febe114b2593c9671c73a862fd0abd3d2f855), ['hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/gata1/gata1_theta.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/gata1/gata1_variants.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/jak1/jak1_cell_metadata.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/jak1/jak1_gene_info.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/jak1/jak1_theta.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/jak1/metadata_genotyped_experiment.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_KRAS.processed.cells.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_KRAS.processed.cells.metadata.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_KRAS.processed.genes.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_KRAS.variants2cell.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_TP53.processed.cells.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_TP53.processed.cells.metadata.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_TP53.processed.genes.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/allele/ursu_gse161824/GSE161824_A549_TP53.variants2cell.csv.gz', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/benchmark/allele_perturb_bench.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/external/scperturb/manifest.tsv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/external/vcc/gene_names.csv', 'hf://datasets/Boom5426/PertResolve_Bench@132febe114b2593c9671c73a862fd0abd3d2f855/external/vcc/pert_counts_Validation.csv']
              
              Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)

Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.

mutation_name string	n_cells int64	is_wt bool	n_aa_changes int64	aa_changes string	positions string	primary_position int64	in_holdout1 bool	in_holdout2 bool	in_holdout3 bool	in_holdout4 bool	in_holdout5 bool	d_hydro float64	d_vol float64	d_charge float64	fold_core float64	cat_switch float64	is_hotspot float64	severity_dist float64	clinvar_pathogenic float64
C110R	382	false	1	C110R	[110]	110	false	true	false	false	true	-7	64.9	1	0	0	0	2.496671	0
C199R	1,048	false	1	C199R	[199]	199	true	false	false	true	false	-7	64.9	1	0	0	0	1.598352	0
C204R	964	false	1	C204R	[204]	204	false	false	false	false	false	-7	64.9	1	1	1	0	3.303736	0
C204R,V205A	229	false	2	C204R;V205A	[204, 205]	204	false	false	false	true	false	-4.7	6.75	0.5	1	1	0	3.01214	0
C207R	272	false	1	C207R	[207]	207	true	false	false	false	false	-7	64.9	1	1	1	1	6.016796	0
C225R	310	false	1	C225R	[225]	225	true	true	false	false	false	-7	64.9	1	1	1	0	3.216254	0
C228R	645	false	1	C228R	[228]	228	false	true	false	false	false	-7	64.9	1	1	1	0	1.841601	0
C258R	265	false	1	C258R	[258]	258	false	false	true	false	false	-7	64.9	1	1	1	0	2.900849	0
C261R	463	false	1	C261R	[261]	261	false	false	false	false	false	-7	64.9	1	1	1	0	2.335826	0
C346R	190	false	1	C346R	[346]	346	false	false	false	false	false	-7	64.9	1	0	0	0	3.517259	0
D115G	238	false	1	D115G	[115]	115	false	false	false	false	true	3.1	-51	1	0	0	1	3.876232	0
D123G	329	false	1	D123G	[123]	123	false	false	false	true	false	3.1	-51	1	0	0	1	4.709254	0
D125G	269	false	1	D125G	[125]	125	false	false	true	false	false	3.1	-51	1	0	0	0	2.740356	0
D144G	560	false	1	D144G	[144]	144	false	false	false	false	false	3.1	-51	1	0	0	0	2.135896	0
D276G	215	false	1	D276G	[276]	276	false	false	false	false	false	3.1	-51	1	1	0	0	3.632718	0
D65G	329	false	1	D65G	[65]	65	false	false	false	false	true	3.1	-51	1	0	0	0	2.825527	0
E114G	167	false	1	E114G	[114]	114	true	false	false	false	false	3.1	-78.3	1	0	0	0	3.592893	0
E114G,D115G	93	false	2	E114G;D115G	[114, 115]	114	false	false	false	false	false	3.1	-64.65	1	0	0	1	4.874116	0
E122G,D123G	359	false	2	E122G;D123G	[122, 123]	122	false	false	false	true	true	3.1	-64.65	1	0	0	0	2.532322	0
E134G	149	false	1	E134G	[134]	134	false	true	false	false	false	3.1	-78.3	1	0	0	1	4.02601	0
E134G,T135A	267	false	2	E134G;T135A	[134, 135]	134	false	true	false	false	false	2.8	-52.9	0.5	0	0	0	2.762132	0
E13G	157	false	1	E13G	[13]	13	false	true	false	false	false	3.1	-78.3	1	0	0	1	3.847885	0
E200G	932	false	1	E200G	[200]	200	true	false	false	false	false	3.1	-78.3	1	0.5	0	0	1.825011	0
E203G	634	false	1	E203G	[203]	203	false	true	false	false	true	3.1	-78.3	1	0.5	0	0	2.00196	0
E2G	853	false	1	E2G	[2]	2	false	false	false	false	false	3.1	-78.3	1	0	0	0	1.743318	0
E328G	804	false	1	E328G	[328]	328	true	false	false	true	false	3.1	-78.3	1	0.5	0	0	1.68191	0
E348G	347	false	1	E348G	[348]	348	true	true	false	false	true	3.1	-78.3	1	0	0	0	2.981879	0
E39G	692	false	1	E39G	[39]	39	false	false	false	false	false	3.1	-78.3	1	0	0	1	1.763302	1
E85G	473	false	1	E85G	[85]	85	false	false	false	true	true	3.1	-78.3	1	0	0	0	2.179851	0
F168P	125	false	1	F168P	[168]	168	false	false	false	false	false	-4.4	-77.2	0	0	0	1	3.928155	0
F172L	174	false	1	F172L	[172]	172	false	false	false	true	false	1	-23.2	0	0	0	1	4.522846	0
F172P	201	false	1	F172P	[172]	172	true	true	false	true	false	-4.4	-77.2	0	0	0	1	3.798278	0
F172S,F173P	69	false	2	F172S;F173P	[172, 173]	172	false	true	false	true	false	-4	-89.05	0	0	0	1	5.158136	0
F18P	358	false	1	F18P	[18]	18	false	false	true	false	false	-4.4	-77.2	0	0	0	0	2.489158	0
F33P,F34P	72	false	2	F33P;F34P	[33, 34]	33	false	false	false	false	false	-4.4	-77.2	0	0	0	1	5.492271	0
F382S	296	false	1	F382S	[382]	382	false	true	false	false	false	-3.6	-100.9	0	0	0	1	4.254209	0
F394P	782	false	1	F394P	[394]	394	false	false	false	false	false	-4.4	-77.2	0	0	0	0	1.77367	0
F3L	176	false	1	F3L	[3]	3	false	false	true	false	false	1	-23.2	0	0	0	1	4.673804	0
F3P	448	false	1	F3P	[3]	3	false	true	false	false	false	-4.4	-77.2	0	0	0	0	2.19188	0
F75P	555	false	1	F75P	[75]	75	false	true	false	false	false	-4.4	-77.2	0	0	0	0	2.111512	0
H222R	131	false	1	H222R	[222]	222	true	true	false	false	false	-1.3	20.2	0.9	1	0	1	5.29842	0
H222R,Y223C	529	false	2	H222R;Y223C	[222, 223]	222	false	false	false	false	false	1.25	-32.45	0.45	1	0	0	2.210088	0
H232R,K233E	215	false	2	H232R;K233E	[232, 233]	232	false	false	false	false	false	-0.45	-5	-0.55	0.5	0	0	3.566812	0
H289R	345	false	1	H289R	[289]	289	false	false	false	true	false	-1.3	20.2	0.9	0.5	0	0	2.901513	0
H362R	785	false	1	H362R	[362]	362	false	false	false	false	true	-1.3	20.2	0.9	0	0	0	1.833246	0
H378R	493	false	1	H378R	[378]	378	false	false	false	false	false	-1.3	20.2	0.9	0	0	0	2.386509	0
I242T	225	false	1	I242T	[242]	242	false	false	false	false	true	-5.2	-50.6	0	0.5	0	1	4.460235	0
I242V	488	false	1	I242V	[242]	242	false	false	false	false	false	-0.3	-26.7	0	0.5	0	0	2.230473	0
I249T	175	false	1	I249T	[249]	249	false	true	true	false	false	-5.2	-50.6	0	0.5	0	1	4.007984	0
I249T,V250A	307	false	2	I249T;V250A	[249, 250]	249	true	true	false	false	false	-3.8	-51	0	0.5	0	0	2.827805	0
I249V	330	false	1	I249V	[249]	249	false	false	false	false	false	-0.3	-26.7	0	0.5	0	0	2.877807	0
I302T	307	false	1	I302T	[302]	302	false	false	false	false	false	-5.2	-50.6	0	0.5	0	1	4.227463	0
I302V	159	false	1	I302V	[302]	302	false	false	false	false	true	-0.3	-26.7	0	0.5	0	1	4.568495	0
I87T	341	false	1	I87T	[87]	87	true	false	false	true	false	-5.2	-50.6	0	0	0	0	3.001166	0
K100G,T101A	117	false	2	K100G;T101A	[100, 101]	100	true	false	true	false	false	3	-68	-0.5	0	0	1	4.169681	0
K137E	425	false	1	K137E	[137]	137	true	false	false	false	true	0.4	-30.2	-2	0	0	0	2.274599	0
K137G	342	false	1	K137G	[137]	137	false	false	false	false	false	3.5	-108.5	-1	0	0	0	3.256936	0
K233R,M234V	289	false	2	K233R;M234V	[233, 234]	233	false	false	true	false	false	0.85	-9.05	0	0.5	0	0	2.661863	0
K245G	112	false	1	K245G	[245]	245	false	true	true	false	true	3.5	-108.5	-1	0.5	0	1	5.609461	0
K252G	205	false	1	K252G	[252]	252	false	true	false	false	false	3.5	-108.5	-1	0.5	0	0	3.502716	0
K252R	198	false	1	K252R	[252]	252	false	false	false	false	false	-0.6	4.8	0	0.5	0	1	3.779491	0
K287G	143	false	1	K287G	[287]	287	true	false	false	false	true	3.5	-108.5	-1	0.5	0	1	4.027272	0
K299E	308	false	1	K299E	[299]	299	false	false	false	false	false	0.4	-30.2	-2	0.5	0	0	2.884346	0
K299R,D300G	229	false	2	K299R;D300G	[299, 300]	299	true	false	true	false	false	1.25	-23.1	0.5	0.5	0	0	3.501796	0
K308G	501	false	1	K308G	[308]	308	false	false	false	false	false	3.5	-108.5	-1	0.5	0	0	2.225889	0
K312G	198	false	1	K312G	[312]	312	false	false	true	false	false	3.5	-108.5	-1	0.5	0	1	4.291649	0
K312R	173	false	1	K312R	[312]	312	true	true	false	false	false	-0.6	4.8	0	0.5	0	1	3.951409	0
K314R,K315G	114	false	2	K314R;K315G	[314, 315]	314	false	false	false	false	false	1.45	-51.85	-0.5	0.5	0	1	4.070587	0
K316G	516	false	1	K316G	[316]	316	false	true	false	true	false	3.5	-108.5	-1	0.5	0	0	2.847993	0
K316R	248	false	1	K316R	[316]	316	false	false	true	false	false	-0.6	4.8	0	0.5	0	0	2.926925	0
L103P	438	false	1	L103P	[103]	103	false	false	false	true	true	-5.4	-54	0	0	0	0	2.628322	0
L103P,Y104H	249	false	2	L103P;Y104H	[103, 104]	103	false	false	false	false	false	-3.65	-47.2	0.05	0	0	0	3.181871	0
L124P	1,138	false	1	L124P	[124]	124	false	false	false	false	true	-5.4	-54	0	0	0	0	1.727558	0
L133P	351	false	1	L133P	[133]	133	false	false	false	true	false	-5.4	-54	0	0	0	0	2.479615	0
L136P	418	false	1	L136P	[136]	136	false	false	false	false	false	-5.4	-54	0	0	0	0	2.54005	0
L136S	115	false	1	L136S	[136]	136	false	false	false	false	false	-4.6	-77.7	0	0	0	1	4.892318	0
L141P	166	false	1	L141P	[141]	141	false	false	false	false	false	-5.4	-54	0	0	0	0	3.406837	0
L145P	346	false	1	L145P	[145]	145	false	false	false	true	false	-5.4	-54	0	0	0	1	4.507674	0
L146P	402	false	1	L146P	[146]	146	true	false	false	false	false	-5.4	-54	0	0	0	0	2.793361	0
L148P	1,096	false	1	L148P	[148]	148	false	false	false	true	false	-5.4	-54	0	0	0	0	1.586471	0
L152P	416	false	1	L152P	[152]	152	false	false	false	false	false	-5.4	-54	0	0	0	0	2.354519	0
L156P	268	false	1	L156P	[156]	156	false	true	true	false	false	-5.4	-54	0	0	0	0	3.30705	0
L180P	1,501	false	1	L180P	[180]	180	false	true	true	false	false	-5.4	-54	0	0	0	0	1.549713	0
L190P	393	false	1	L190P	[190]	190	true	false	true	false	true	-5.4	-54	0	0	0	0	2.631343	0
L194P	600	false	1	L194P	[194]	194	false	false	false	true	false	-5.4	-54	0	0	0	0	2.126254	0
L196P	196	false	1	L196P	[196]	196	false	false	false	true	false	-5.4	-54	0	0	0	1	4.24863	0
L214P,W215R	327	false	2	L214P;W215R	[214, 215]	214	false	true	true	false	false	-4.5	-54.2	0.5	1	0	0	2.635395	0
L224P	325	false	1	L224P	[224]	224	true	true	false	true	false	-5.4	-54	0	1	0	0	3.664788	0
L230P,Y231H	243	false	2	L230P;Y231H	[230, 231]	230	false	false	true	false	false	-3.65	-47.2	0.05	0.5	0	0	3.510375	0
L248P	646	false	1	L248P	[248]	248	false	true	false	false	false	-5.4	-54	0	0.5	0	0	2.282715	0
L268P,W269R	538	false	2	L268P;W269R	[268, 269]	268	false	false	false	false	false	-4.5	-54.2	0.5	1	0	0	1.995299	0
L284P,Y285H	71	false	2	L284P;Y285H	[284, 285]	284	false	false	false	false	false	-3.65	-47.2	0.05	0.5	0	1	6.778019	0
L288P	413	false	1	L288P	[288]	288	false	false	false	false	true	-5.4	-54	0	0.5	0	0	2.830554	0
L295P	319	false	1	L295P	[295]	295	false	false	false	false	false	-5.4	-54	0	0.5	0	0	2.637356	0
L355P	311	false	1	L355P	[355]	355	true	false	false	false	false	-5.4	-54	0	0	0	0	3.210804	0
L363P	650	false	1	L363P	[363]	363	true	false	false	false	false	-5.4	-54	0	0	0	0	1.927685	0
L363P,Y364H	559	false	2	L363P;Y364H	[363, 364]	363	false	false	false	false	true	-3.65	-47.2	0.05	0	0	0	2.290156	0
L367P	1,080	false	1	L367P	[367]	367	false	false	false	false	true	-5.4	-54	0	0	0	0	2.429928	0
L372P,S373P	420	false	2	L372P;S373P	[372, 373]	372	false	true	false	false	false	-3.1	-15.15	0	0	0	0	2.306328	0
L379P	289	false	1	L379P	[379]	379	false	true	false	false	false	-5.4	-54	0	0	0	0	2.892194	0

End of preview.

PertResolve-Bench datasets

This repository contains the allele-resolved data and the public perturbation datasets used by the PertResolve manuscript. It is a data release only: it does not contain the manuscript figures, analysis code, model predictions, or the results/ directory. The corresponding code and result reports remain in the PertResolve GitHub repository.

Included data

Allele-resolved benchmark

benchmark/allele_perturb_bench.csv: 470 protein-coding variant conditions plus two wild-type reference rows, with gene, protein, biophysical features, cell counts and evaluation partitions.
benchmark/hotspot_external_definition.txt: external hotspot definition used by the benchmark annotations.
benchmark/supplementary_data_1_datasets.xlsx: the Supplementary Data 1 inventory and source metadata.

The complete compact allele package is included:

TP53 and KRAS (GSE161824): processed cell-by-gene matrices, cell and gene tables, cell metadata and variants2cell assignments under allele/ursu_gse161824/. Source: GEO GSE161824.
GATA1 (GSE215253/PerturbNet processing): allele/gata1/GATA1_standard_hvg_pert_filtered.h5ad, variant and theta tables, and the processed array under allele/gata1_arrays.npz. Source: GEO GSE215253 and the PerturbNet repository.
JAK1 (scSNV-seq): the genotyped single-cell object allele/jak1/sce_genotyped.rds, cell/gene/experiment metadata, theta table and allele/jak1_arrays.npz. Sources: ENA PRJEB48915 and Zenodo record 10418435.
allele/joint_arrays.npz, allele/real_deltas.npz and allele/barcode_rebuild_provenance.json: compact processed products and provenance for the allele analyses.
allele/esm1v_embeddings.npz: ESM-1v variant embeddings used as molecular features. Model weights are not redistributed; cite and follow the terms of FAIR ESM and Meier et al. (2021).

Broader perturbation panel

The following paper-used resources are included when their complete source resource is below the 100 GB release threshold:

external/scperturb/: selected scPerturb h5ad objects for Norman, Replogle K562 essential, Adamson, McFarland, Frangieh RNA/protein, Papalexi ECCITE RNA/protein and sciPlex3, together with the source manifest. Source: scPerturb Zenodo record 10044268.
external/vcc/adata_Training.h5ad and its small validation/gene-name tables: the VCC training object used in the paper. Source: Arc Virtual Cell Atlas and the associated Cell paper (DOI 10.1016/j.cell.2025.06.008).
external/gse306429/: the combined demultiplexed single-cell object and processed score/pseudobulk objects from GSE306429. Source: GEO GSE306429.
external/perturbmulti/: processed CRISPR RNA and protein objects and the source README for PerturbMulti. Source: GEO GSE275483; the source README identifies the processed release as CC BY 4.0.

Files are stored in their native spaces. No results/ tables, differential- expression result objects, model checkpoints, prediction arrays, figures or analysis scripts are included.

Deliberate exclusions

Resources whose complete source resource exceeds 100 GB are not mirrored in this repository. Their provenance is retained here so that they can be retrieved from the original providers:

Tahoe-100M full h5ad collection (about 320 GB),
X-Atlas/Orion (about 118 GB),
the KOLF pan-genome object (about 234 GB; see the Arc Virtual Cell Atlas release), and
the Parse 10M PBMC object (about 212 GB; source/hosting details are given in the PertResolve manuscript and its preregistration).

The protocol-excluded non-cell-level CIGS and cpg0016 resources are also not included. These exclusions do not remove the corresponding benchmark definitions from the manuscript; they only avoid redistributing very large or out-of-scope source resources.

Provenance, licensing and citation

The Hugging Face repository is marked license: other because it combines author-generated annotations/derived products with files derived from public third-party datasets. This label is intentional and is not an Apache-2.0 grant for the third-party files. The original provider terms and attribution requirements apply to each source dataset; see NOTICE, the source manifests and per-resource source notes. The benchmark metadata and provenance text written for this release may be reused with attribution to the PertResolve authors, but no underlying third-party data are relicensed.

Please cite the PertResolve manuscript and the original source records listed above when using these data. MANIFEST.sha256 records the checksum of every included data or metadata file.

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