| 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) | |
| ``` |