Datasets:

Genentech
/

human-atac-catlas-data

license: mit
task_categories:
  - tabular-classification
tags:
  - biology
  - genomics
pretty_name: CATlas Human Enhancer Binary Matrix
size_categories:
  - 1M<n<10M

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

data.h5ad: The main dataset stored in AnnData format.
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)