Error code:   ConfigNamesError
Exception:    FileNotFoundError
Message:      Couldn't find any data file at /src/services/worker/nicolas-lynn/vcell-perturbation-panel. Couldn't find 'nicolas-lynn/vcell-perturbation-panel' on the Hugging Face Hub either: FileNotFoundError: Unable to find 'hf://datasets/nicolas-lynn/vcell-perturbation-panel@5ad002c8980f4c82b64ceae66ce6391ea25bd937/panel_pb1.h5ad' with any supported extension ['.csv', '.tsv', '.json', '.jsonl', '.ndjson', '.parquet', '.geoparquet', '.gpq', '.arrow', '.txt', '.tar', '.xml', '.hdf5', '.h5', '.eval', '.lance', '.blp', '.bmp', '.dib', '.bufr', '.cur', '.pcx', '.dcx', '.dds', '.ps', '.eps', '.fit', '.fits', '.fli', '.flc', '.ftc', '.ftu', '.gbr', '.gif', '.grib', '.png', '.apng', '.jp2', '.j2k', '.jpc', '.jpf', '.jpx', '.j2c', '.icns', '.ico', '.im', '.iim', '.tif', '.tiff', '.jfif', '.jpe', '.jpg', '.jpeg', '.mpg', '.mpeg', '.msp', '.pcd', '.pxr', '.pbm', '.pgm', '.ppm', '.pnm', '.psd', '.bw', '.rgb', '.rgba', '.sgi', '.ras', '.tga', '.icb', '.vda', '.vst', '.webp', '.wmf', '.emf', '.xbm', '.xpm', '.BLP', '.BMP', '.DIB', '.BUFR', '.CUR', '.PCX', '.DCX', '.DDS', '.PS', '.EPS', '.FIT', '.FITS', '.FLI', '.FLC', '.FTC', '.FTU', '.GBR', '.GIF', '.GRIB', '.PNG', '.APNG', '.JP2', '.J2K', '.JPC', '.JPF', '.JPX', '.J2C', '.ICNS', '.ICO', '.IM', '.IIM', '.TIF', '.TIFF', '.JFIF', '.JPE', '.JPG', '.JPEG', '.MPG', '.MPEG', '.MSP', '.PCD', '.PXR', '.PBM', '.PGM', '.PPM', '.PNM', '.PSD', '.BW', '.RGB', '.RGBA', '.SGI', '.RAS', '.TGA', '.ICB', '.VDA', '.VST', '.WEBP', '.WMF', '.EMF', '.XBM', '.XPM', '.aiff', '.au', '.avr', '.caf', '.flac', '.htk', '.svx', '.mat4', '.mat5', '.mpc2k', '.ogg', '.paf', '.pvf', '.raw', '.rf64', '.sd2', '.sds', '.ircam', '.voc', '.w64', '.wav', '.nist', '.wavex', '.wve', '.xi', '.mp3', '.opus', '.3gp', '.3g2', '.avi', '.asf', '.flv', '.mp4', '.mov', '.m4v', '.mkv', '.webm', '.f4v', '.wmv', '.wma', '.ogm', '.mxf', '.nut', '.AIFF', '.AU', '.AVR', '.CAF', '.FLAC', '.HTK', '.SVX', '.MAT4', '.MAT5', '.MPC2K', '.OGG', '.PAF', '.PVF', '.RAW', '.RF64', '.SD2', '.SDS', '.IRCAM', '.VOC', '.W64', '.WAV', '.NIST', '.WAVEX', '.WVE', '.XI', '.MP3', '.OPUS', '.3GP', '.3G2', '.AVI', '.ASF', '.FLV', '.MP4', '.MOV', '.M4V', '.MKV', '.WEBM', '.F4V', '.WMV', '.WMA', '.OGM', '.MXF', '.NUT', '.pdf', '.PDF', '.nii', '.NII', '.zip', '.idx', '.manifest', '.txn']
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/dataset/config_names.py", line 67, in compute_config_names_response
                  config_names = get_dataset_config_names(
                                 ^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/inspect.py", line 161, in get_dataset_config_names
                  dataset_module = dataset_module_factory(
                                   ^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/load.py", line 1203, in dataset_module_factory
                  raise FileNotFoundError(
              FileNotFoundError: Couldn't find any data file at /src/services/worker/nicolas-lynn/vcell-perturbation-panel. Couldn't find 'nicolas-lynn/vcell-perturbation-panel' on the Hugging Face Hub either: FileNotFoundError: Unable to find 'hf://datasets/nicolas-lynn/vcell-perturbation-panel@5ad002c8980f4c82b64ceae66ce6391ea25bd937/panel_pb1.h5ad' with any supported extension ['.csv', '.tsv', '.json', '.jsonl', '.ndjson', '.parquet', '.geoparquet', '.gpq', '.arrow', '.txt', '.tar', '.xml', '.hdf5', '.h5', '.eval', '.lance', '.blp', '.bmp', '.dib', '.bufr', '.cur', '.pcx', '.dcx', '.dds', '.ps', '.eps', '.fit', '.fits', '.fli', '.flc', '.ftc', '.ftu', '.gbr', '.gif', '.grib', '.png', '.apng', '.jp2', '.j2k', '.jpc', '.jpf', '.jpx', '.j2c', '.icns', '.ico', '.im', '.iim', '.tif', '.tiff', '.jfif', '.jpe', '.jpg', '.jpeg', '.mpg', '.mpeg', '.msp', '.pcd', '.pxr', '.pbm', '.pgm', '.ppm', '.pnm', '.psd', '.bw', '.rgb', '.rgba', '.sgi', '.ras', '.tga', '.icb', '.vda', '.vst', '.webp', '.wmf', '.emf', '.xbm', '.xpm', '.BLP', '.BMP', '.DIB', '.BUFR', '.CUR', '.PCX', '.DCX', '.DDS', '.PS', '.EPS', '.FIT', '.FITS', '.FLI', '.FLC', '.FTC', '.FTU', '.GBR', '.GIF', '.GRIB', '.PNG', '.APNG', '.JP2', '.J2K', '.JPC', '.JPF', '.JPX', '.J2C', '.ICNS', '.ICO', '.IM', '.IIM', '.TIF', '.TIFF', '.JFIF', '.JPE', '.JPG', '.JPEG', '.MPG', '.MPEG', '.MSP', '.PCD', '.PXR', '.PBM', '.PGM', '.PPM', '.PNM', '.PSD', '.BW', '.RGB', '.RGBA', '.SGI', '.RAS', '.TGA', '.ICB', '.VDA', '.VST', '.WEBP', '.WMF', '.EMF', '.XBM', '.XPM', '.aiff', '.au', '.avr', '.caf', '.flac', '.htk', '.svx', '.mat4', '.mat5', '.mpc2k', '.ogg', '.paf', '.pvf', '.raw', '.rf64', '.sd2', '.sds', '.ircam', '.voc', '.w64', '.wav', '.nist', '.wavex', '.wve', '.xi', '.mp3', '.opus', '.3gp', '.3g2', '.avi', '.asf', '.flv', '.mp4', '.mov', '.m4v', '.mkv', '.webm', '.f4v', '.wmv', '.wma', '.ogm', '.mxf', '.nut', '.AIFF', '.AU', '.AVR', '.CAF', '.FLAC', '.HTK', '.SVX', '.MAT4', '.MAT5', '.MPC2K', '.OGG', '.PAF', '.PVF', '.RAW', '.RF64', '.SD2', '.SDS', '.IRCAM', '.VOC', '.W64', '.WAV', '.NIST', '.WAVEX', '.WVE', '.XI', '.MP3', '.OPUS', '.3GP', '.3G2', '.AVI', '.ASF', '.FLV', '.MP4', '.MOV', '.M4V', '.MKV', '.WEBM', '.F4V', '.WMV', '.WMA', '.OGM', '.MXF', '.NUT', '.pdf', '.PDF', '.nii', '.NII', '.zip', '.idx', '.manifest', '.txn']

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ConvergeCELL Pseudobulk Panel — v1.0.0

Multi-tissue, multi-cell-type pseudobulk library built from public single-cell RNA-seq datasets. Each pseudobulk size (1 / 5 / 10 / 20 cells) is published as a separate H5AD; downstream code picks the granularity that fits the task.

What's in each file

File	Rows	Genes	Cells per pseudobulk	# pseudobulks per (dataset, cell_type)	# (dataset, cell_type) combos	Bootstrap rows	Aggregation
`panel_pb1.h5ad`	4,610	75,098	1	5	922	0	sum
`panel_pb10.h5ad`	4,610	75,098	10	5	922	735	sum
`panel_pb20.h5ad`	4,610	75,098	20	5	922	1340	sum
`panel_pb5.h5ad`	4,610	75,098	5	5	922	0	sum

Schema

obs (per pseudobulk)

Column	Type	Meaning
`sample_id`	str (index)	Unique identifier `{dataset}__{cell_type}__pb{i}__size{n}`
`dataset`	str	Source dataset name
`tissue`	str	Tissue label
`cell_type`	str	Cell type label as annotated in the source dataset
`pseudobulk_id`	int	0..n_pb_per_combo − 1
`cells_per_pb`	int	Aggregation size
`n_avail_cells`	int	# cells of this type in the source dataset
`bootstrap`	bool	`True` if sampling-with-replacement was needed

var (per gene)

Column	Type	Meaning
`gene_symbol`	str (index)	HGNC symbol
`n_datasets_present`	int	# source datasets that contained this gene

uns

panel_version, seed, cells_per_pb, n_pb_per_combo, min_cells, aggregation, source_datasets

Tissues covered

bladder, blood, bone_marrow, eye, fat, heart, islet, kidney, liver, lung, skin, spleen

Source datasets

bladder_gouin
melanoma_tirosh
skin_healthy
ts_blood
ts_bone_marrow
ts_eye
ts_fat
ts_heart
ts_kidney
ts_liver
ts_lung
ts_pancreas
ts_skin
ts_spleen

How to load

from huggingface_hub import hf_hub_download
import anndata as ad

path = hf_hub_download(
    repo_id="nicolas-lynn/vcell-perturbation-panel",
    filename="panel_pb20.h5ad",       # or panel_pb1 / pb5 / pb10
    repo_type="dataset",
)
adata = ad.read_h5ad(path)

To fetch all sizes:

from huggingface_hub import snapshot_download
local = snapshot_download(repo_id="nicolas-lynn/vcell-perturbation-panel", repo_type="dataset")
# local/panel_pb1.h5ad, panel_pb5.h5ad, panel_pb10.h5ad, panel_pb20.h5ad

Reproducibility

Built by convergecell-data (seed = 0, deterministic). Re-running convergecell-build-panel on the same source datasets produces bit-identical files.

License

CC BY 4.0. Source single-cell datasets retain their original licenses — see each dataset's primary publication.

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Total file size:

5.56 GB