| --- |
| license: mit |
| task_categories: |
| - tabular-regression |
| tags: |
| - biology |
| - genomics |
| pretty_name: "gReLU tutorial 3 dataset (Microglia scATAC-seq)" |
| size_categories: |
| - 10K<n<100K |
| --- |
| |
| # microglia-scatac-tutorial-data |
|
|
| ## Dataset Summary |
| This dataset contains pseudobulk scATAC-seq data for human microglia, derived from the study by Corces et al. (2020) (https://www.nature.com/articles/s41588-020-00721-x). Genome coordinates correspond to the hg38 reference genome. This data is used in tutorial 3 of gReLU (https://github.com/Genentech/gReLU/blob/main/docs/tutorials/3_train.ipynb). |
| |
| ## Dataset Structure |
| |
| The dataset is divided into two files: peaks and fragments. |
| |
| ### Statistics |
| | File | Rows | Description | |
| |------|------|-------------| |
| | `peak_file.narrowPeak` | 83,320 | Called ATAC-seq peaks | |
| | `fragment_file.bed` | 57,919,016 | Individual ATAC-seq fragments | |
|
|
| ### 1. Peaks file (`peak_file.narrowPeak`) |
| Standard ENCODE narrowPeak format (tab-separated, no header). |
| - `chrom`: Chromosome / Contig name |
| - `start`: 0-based start position |
| - `end`: End position |
| - `name`: Peak identifier |
| - `score`: Integer score for display |
| - `strand`: Orientation |
| - `signalValue`: Measurement of overall enrichment |
| - `pValue`: Statistical significance (-log10) |
| - `qValue`: False discovery rate (-log10) |
| - `peak`: Point-source (summit) relative to start |
| |
| ### 2. Fragments file (`fragment_file.bed`) |
| Standard BED6 format representing individual ATAC-seq fragments. |
| - `chrom`: Chromosome |
| - `start`: Start position |
| - `end`: End position |
| - `source`: Sequencing run identifier (e.g., `SRR11442505`) |
| - `score`: Placeholder (0) |
| - `strand`: Orientation |
|
|
| ## Usage |
|
|
| ```python |
| from huggingface_hub import hf_hub_download |
| import pandas as pd |
| |
| peak_path = hf_hub_download( |
| repo_id="Genentech/microglia-scatac-tutorial-data", |
| repo_type="dataset", |
| filename="peak_file.narrowPeak" |
| ) |
| peaks = pd.read_csv(peak_path, sep='\t', header=None) |
| |
| frag_path = hf_hub_download( |
| repo_id="Genentech/microglia-scatac-tutorial-data", |
| repo_type="dataset", |
| filename="fragment_file.bed" |
| ) |
| fragments = pd.read_csv(frag_path, sep='\t', header=None, |
| names=['chrom', 'start', 'end', 'source', 'score', 'strand']) |
| ``` |
|
|
