Datasets:

Genentech
/

binary-atac-tutorial-data

license: mit
task_categories:
  - tabular-classification
tags:
  - biology
  - genomics
pretty_name: gReLU Tutorial 2 dataset
size_categories:
  - 1M<n<10M

tutorial-2-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", filename="data.h5ad")
ada = anndata.read_h5ad(file_path)