| --- |
| 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`](https://doi.org/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`](https://doi.org/10.1101/2024.11.03.621734) | |
| | **Analysis code** | https://github.com/y-doctor/KOLF2.1J_Perturbation_Cell_Atlas (MIT) | |
| |
| ## Files |
| |
| All files are [AnnData](https://anndata.readthedocs.io/) `.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 |
|
|
| ```python |
| 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: |
|
|
| ```bibtex |
| @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`](https://doi.org/10.25452/figshare.plus.27261219.v1). CC BY 4.0. |
|
|
