nicolas-lynn/vcell-perturbation-source-data

ConvergeCELL Source Datasets — v1.0.0

Cached H5ADs of every single-cell RNA-seq dataset registered in the ConvergeCELL data catalog. Mirrors the original sources (GEO, figshare, Tabula Sapiens, CellxGene) so downstream code has a single, fast, versioned endpoint to fetch from.

Each row of every h5ad is one cell; each column is one gene (HGNC symbol). The exact obs/var schema follows whatever the original source provided — this bundle does not re-annotate, harmonize, or QC. For a harmonized, pseudobulked variant see converge-bio/pseudobulk-panel-v1.

Datasets (18)

Name	Tissue	Disease	# Cells	# Cell Types	Accession	Publication
bladder_gouin	bladder	urothelial_carcinoma	67,988	5	GSE169379	Gouin et al., Nature Communications 2021
bladder_gouin_normal	bladder	healthy	25,102	—	GSE169379	Gouin et al., Nature Communications 2021
bladder_lai	bladder	urothelial_carcinoma	36,788	—	GSE135337	Lai et al., Int J Cancer 2021
melanoma_jerby_arnon	skin	melanoma	7,186	—	GSE115978	Jerby-Arnon et al., Cell 2018
melanoma_sade_feldman	skin	melanoma	16,291	—	GSE120575	Sade-Feldman et al., Cell 2018
melanoma_tirosh	skin	melanoma	4,645	7	GSE72056	Tirosh et al., Science 2016
pbmc3k	blood	healthy	2,700	—	N/A	10X Genomics
skin_healthy	skin	healthy	50,000	127	CellxGene	CellxGene
ts_blood	blood	healthy	10,000	107	figshare:14267219	Tabula Sapiens Consortium, Science 2022
ts_bone_marrow	bone_marrow	healthy	10,000	119	figshare:14267219	Tabula Sapiens Consortium, Science 2022
ts_eye	eye	healthy	10,000	105	figshare:14267219	Tabula Sapiens Consortium, Science 2022
ts_heart	heart	healthy	10,000	67	figshare:14267219	Tabula Sapiens Consortium, Science 2022
ts_kidney	kidney	healthy	10,000	114	figshare:14267219	Tabula Sapiens Consortium, Science 2022
ts_liver	liver	healthy	10,000	117	figshare:14267219	Tabula Sapiens Consortium, Science 2022
ts_lung	lung	healthy	10,000	167	figshare:14267219	Tabula Sapiens Consortium, Science 2022
ts_pancreas	islet	healthy	10,000	54	figshare:14267219	Tabula Sapiens Consortium, Science 2022
ts_skin	skin	healthy	10,000	105	figshare:14267219	Tabula Sapiens Consortium, Science 2022
ts_spleen	spleen	healthy	10,000	90	figshare:14267219	Tabula Sapiens Consortium, Science 2022

How to load

from huggingface_hub import hf_hub_download
import anndata as ad

path = hf_hub_download(
    repo_id="nicolas-lynn/vcell-perturbation-source-data",
    filename="ts_lung.h5ad",     # any name from the table above
    repo_type="dataset",
)
adata = ad.read_h5ad(path)

Or, programmatically via convergecell-data which will fall back to HF when the local cache is empty:

import convergecell_data as cd
adata = cd.load_dataset("ts_lung")

License

CC BY 4.0 for the manifest + dataset card. Each individual h5ad retains its upstream license — consult the publication column for the canonical source.