Genentech/human-atac-catlas-data

human-catlas-atac-data

Dataset Summary

This dataset provides a binary accessibility matrix of candidate Cis-Regulatory Elements (cCREs) across human cell types. It is derived from the CATlas project (https://decoder-genetics.wustl.edu/catlasv1/catlas_humanenhancer/#!/). The matrix identifies which genomic regions are accessible (1) or inaccessible (0) across 204 distinct cell types. The data is derived from https://decoder-genetics.wustl.edu/catlasv1/humanenhancer/data/cCRE_by_cell_type/. The hg38 genome build was used.

Repository Content

1. data.h5ad: The main dataset stored in AnnData format.
2. 1_data.ipynb: Jupyter notebook containing the preprocessing steps used to generate the .h5ad file.

Dataset Structure

AnnData Object Dimensions

• n_obs (Cell Types): 204
• n_vars (cCREs): 1,121,319

Data Fields

• .X: A sparse binary matrix where rows are cell types and columns are genomic regions (cCREs).
• .obs (Cell Type Metadata):
  • cell type: The descriptive name of the human cell type/cluster.
• .var (Genomic Feature Metadata):
  • chrom, start, end: Genomic coordinates (hg38).
  • cre_class: Classification of the regulatory element.
  • in_fetal / in_adult: indicators of activity in developmental stages.
  • cre_module: Associated regulatory module.
  • enformer_split: Overlap with the data splits used for training the Enformer model.
  • split: Splits used for downstream modeling (training/validation/test).

Usage

import anndata as ad
from huggingface_hub import hf_hub_download

file_path = hf_hub_download(
    repo_id="Genentech/human-atac-catlas-data", 
    filename="data.h5ad"
)

ad = anndata.read_h5ad(file_path)