README.md

metadata

license: cc-by-4.0
pretty_name: KOLF2.1J Perturbation Cell Atlas (h5ad)
tags:
  - biology
  - single-cell
  - perturb-seq
  - crispri
  - genomics
  - ipsc
  - anndata
task_categories:
  - feature-extraction

KOLF2.1J Perturbation Cell Atlas — raw .h5ad

This repository is a mirror of the raw AnnData (.h5ad) files from the KOLF2.1J Perturbation Cell Atlas, a genome-scale CRISPRi Perturb-seq atlas of human induced pluripotent stem cells (iPSCs).

This is not original work by the uploader. The data were produced by Doctor, Nourreddine, and Mali, released under CC BY 4.0, and are re-hosted here only to make the raw .h5ad files easier to download. All credit belongs to the original authors; please cite them (see Citation below).

Provenance

Original title	A genome-scale CRISPRi perturbation atlas of human induced pluripotent stem cells
Authors	Yesh Doctor, Sami Nourreddine, Prashant Mali
Source dataset	figshare, DOI 10.25452/figshare.plus.27261219.v1
License	Creative Commons Attribution 4.0 International (CC BY 4.0)
Associated preprint	10.1101/2024.11.03.621734
Analysis code	https://github.com/y-doctor/KOLF2.1J_Perturbation_Cell_Atlas (MIT)

Files

All files are AnnData .h5ad (HDF5). Sizes and MD5 checksums are listed below; verify after download with md5sum.

File	Size	MD5
KOLF_Metabolic_Enzymes_Strong_Perturbations.h5ad	1.23 GB	95f57fd679b98ba4f060d143959c3a66
KOLF_Chromatin_Modifiers_Strong_Perturbations.h5ad	1.42 GB	fbd62eee013ad01be10f8ff291c8f8f5
KOLF_Chromatin_Modifiers_QC_Filtered.h5ad	4.32 GB	246eda29efaf8ae8da86c39840678582
KOLF_Metabolic_Enzymes_QC_Filtered.h5ad	6.50 GB	b5e17ab928cf263f679cf63bbb311a25
KOLF_Strong_Perturbations.h5ad	43.51 GB	28bcfff0679e7c6c35bdd584f3626362
KOLF_Pan_Genome_QC_Filtered.h5ad	176.4 GB	afd30fde1e6ad32969c29868394385d1

checksums.md5 in this repo contains the same checksums in md5sum -c format.

Note on the large file. KOLF_Pan_Genome_QC_Filtered.h5ad is ~176 GiB. Use streaming/backed reads (anndata.read_h5ad(path, backed="r")) unless you have enough RAM to load it in full.

Usage

from huggingface_hub import hf_hub_download
import anndata as ad

path = hf_hub_download(
    repo_id="Boom5426/KOLF",
    repo_type="dataset",
    filename="KOLF_Chromatin_Modifiers_Strong_Perturbations.h5ad",
)
adata = ad.read_h5ad(path, backed="r")
print(adata)

Citation

If you use these data, cite the original authors:

@article{doctor2024kolf,
  title   = {A genome-scale CRISPRi perturbation atlas of human induced pluripotent stem cells},
  author  = {Doctor, Yesh and Nourreddine, Sami and Mali, Prashant},
  journal = {bioRxiv},
  year    = {2024},
  doi     = {10.1101/2024.11.03.621734}
}

Dataset: Doctor Y., Nourreddine S., Mali P. KOLF2.1J Perturbation Cell Atlas. figshare. DOI 10.25452/figshare.plus.27261219.v1. CC BY 4.0.