Datasets:

Genentech
/

GM12878_dnase-data

license: mit
task_categories:
  - tabular-regression
tags:
  - biology
  - genomics
pretty_name: GM12878 DNase regression model
size_categories:
  - 100K<n<1M

GM12878_dnase-data

Dataset Summary

This dataset contains genomic intervals used to train a regression model on GM12878 DNase data, described in Lal et al. 2025 (https://www.nature.com/articles/s41592-025-02868-z). Genome coordinates correspond to the hg38 reference genome.

Repository Content

The repository includes one BED file and one Jupyter notebook:

intervals.bed: Genomic intervals stored in BED format.
1_process_GM12878_data.ipynb: Jupyter notebook containing the preprocessing steps used to generate the intervals.bed file.

Dataset Structure

1. Intervals file (`intervals.bed`)

BED format (tab-separated). There are three columns with no header. All intervals have length 2114 bp.

Chromosome name.
start position.
end position.

Usage

from huggingface_hub import hf_hub_download
import pandas as pd

file_path = hf_hub_download(repo_id="Genentech/GM12878_dnase-data", filename="intervals.bed")
df_human = pd.read_csv(file_path, sep='\t', header=None)