binary-atac-tutorial-data

Dataset Summary

This dataset contains binary accessibility values for 1154611 CREs in 222 cell types. The original source of this data is CATlas (https://decoder-genetics.wustl.edu/catlasv1/humanenhancer/data/cCRE_by_cell_type/). For more details, see https://decoder-genetics.wustl.edu/catlasv1/catlas_humanenhancer/#!/. This version of the dataset is used in gReLU tutorial 2 (https://github.com/Genentech/gReLU/blob/main/docs/tutorials/2_finetune.ipynb).

Dataset Structure

Data Fields

In .obs:

Column	Type	Description
cell type	string	Name of the cell type

In .var:

Column	Type	Description
chrom	string	Chromosome (e.g., chr6)
start	int	Genomic start position (hg38)
end	int	Genomic end position (hg38)
Class	category	CRE class

.X is a binary accessibility matrix of shape (222 × 1154611) in Compressed Sparse Row format.

Usage

import anndata
from huggingface_hub import hf_hub_download

file_path = hf_hub_download(
    repo_id="Genentech/tutorial-2-data",
    repo_type="dataset",
    filename="data.h5ad"
)
ad = anndata.read_h5ad(file_path)