datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
single-cell-brain-zarr
Single-Cell Brain Zarr Collection
Production-ready brain single-cell RNA-seq data exported from the CellxGene Census into native Zarr stores for chunked, on-demand access on the Hugging Face Hub.
Why Zarr
Single-cell expression matrices get impractical fast if you treat them like ordinary dense files. Zarr is the point of this repo: it makes large atlas-scale data usable without forcing users to download or materialize the whole matrix before they can do anything useful.… See the full description on the dataset page: https://huggingface.co/datasets/KokosDev/single-cell-brain-zarr.aging-gene-expression-single-cell-mouse
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
https://www.nature.com/articles/s41586-020-2496-1#Sec2
Code to download and process this dataset is available in: https://github.com/seanome/2025-longevity-x-ai-hackathon
Dataset structure is originally from AnnData.
Descriptions of each data file is below.
Data Files
This dataset contains multiple parquet files, one for each sheet in the original Excel file:… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/aging-gene-expression-single-cell-mouse.single-cell-lung-zarr
Single-cell lung (CellxGene Census) — Zarr
This dataset was exported from the CellxGene Census as a chunked + compressed Zarr store intended for easy streaming access.
Source: CellxGene Census API
Organism: Homo sapiens
Filter: tissue_general == 'lung' and is_primary_data == True
Shape: 100,000 cells × 61,497 genes
Zarr path: lung.zarr
Compression
Uncompressed (dense float32): 22.91 GB
Compressed Zarr: ~307 MB (322 MB on Hub)
Compression ratio: ~76× (Blosc zstd on… See the full description on the dataset page: https://huggingface.co/datasets/KokosDev/single-cell-lung-zarr.gtex-single-cell-rnaseq
GTEx Single-Cell RNA-seq Dataset
This repository provides tools to create a Hugging Face dataset from GTEx single-nucleus RNA-seq data, transforming the hierarchical H5AD format into a flat, ML-ready structure.
Overview
Data Source
The data comes from GTEx's snRNA-seq atlas:
Source: GTEx Portal
Publication: Eraslan et al., Science 2022 - "Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function"
Content: 209… See the full description on the dataset page: https://huggingface.co/datasets/ai-department-lpnu/gtex-single-cell-rnaseq.single-cell.GSM6611298_P14601_4005_barcodessingle-cell_raw
OTAR3088 SingleCell raw data
.zip containing all .json output files from annotations carried out in LabelStudio. These are considered the raw outputs of curation carried out for this data.
The following EuropePMC articles were annotated here:
PMC12081310
PMC11578878
PMC10287567
PMC8809252
PMC12479362
PMC12435838
PMC12408821
PMC12396968
PMC12256823
PMC12116388
PMC12133578
PMC11116453
Annotations were completed in alignment with the following annotation guidelines:… See the full description on the dataset page: https://huggingface.co/datasets/OTAR3088/single-cell_raw.single-cell.GSM6611296_P15306_5002_barcodessingle-cell.GSM6611297_P14601_4004_barcodessingle-cell.GSM6611295_P15306_5001_featuressingle-cell.GSM6611295_P15306_5001_barcodessingle-cell.GSM6611296_P15306_5002_featuressingle-cell.GSM6611298_P14601_4005_featuressingle-cell.GSM6611299_P15306_5003_barcodessingle-cell.GSM6611300_P15306_5004_barcodessingle-cell.GSM6611297_P14601_4004_featuressingle-cell.GSM6611299_P15306_5003_featuressingle-cell.GSM6611300_P15306_5004_features