---
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:
1. `intervals.bed`: Genomic intervals stored in BED format.
2. `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

```python
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)
```