| --- |
| license: cc-by-4.0 |
| language: en |
| tags: [biology, single-cell, transcriptomics, anndata, h5ad, raw-data] |
| size_categories: ['1M<n<10M'] |
| --- |
| |
| # 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](https://huggingface.co/datasets/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 |
|
|
| ```python |
| 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: |
|
|
| ```python |
| 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. |
|
|
