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--- |
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license: mit |
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task_categories: |
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- tabular-regression |
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tags: |
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- biology |
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- genomics |
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pretty_name: "gReLU tutorial 3 dataset (Microglia scATAC-seq)" |
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size_categories: |
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- 10K<n<100K |
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--- |
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# microglia-scatac-tutorial-data |
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## Dataset Summary |
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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). |
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## Dataset Structure |
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The dataset is divided into two configurations: `peaks` and `fragments`. |
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### 1. Peaks Configuration (`peak_file.narrowPeak`) |
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Standard ENCODE narrowPeak format (tab-separated). |
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- `chrom`: Chromosome / Contig name. |
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- `start`: 0-based start position. |
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- `end`: End position. |
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- `name`: Peak identifier. |
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- `score`: Integer score for display. |
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- `strand`: Orientation. |
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- `signalValue`: Measurement of overall enrichment. |
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- `pValue`: Statistical significance (-log10). |
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- `qValue`: False discovery rate (-log10). |
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- `peak`: Point-source (summit) relative to start. |
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### 2. Fragments Configuration (`fragment_file.bed`) |
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Standard BED6 format representing individual ATAC-seq fragments. |
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- `chrom`: Chromosome. |
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- `start`: Start position. |
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- `end`: End position. |
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- `source`: Sequencing run identifier (e.g., `SRR11442505`). |
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- `score`: Placeholder (0). |
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- `strand`: Orientation. |
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## Usage |
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```python |
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from huggingface_hub import hf_hub_download |
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import grelu.io.bed |
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import pandas as pd |
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peak_path = hf_hub_download( |
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repo_id="Genentech/microglia-scatac-tutorial-data", |
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repo_type="dataset", |
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filename="peak_file.narrowPeak" |
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) |
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peaks = grelu.io.bed.read_narrowpeak(peak_file) |
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frag_path = hf_hub_download( |
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repo_id="Genentech/microglia-scatac-tutorial-data", |
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repo_type="dataset", |
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filename="fragment_file.bed" |
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) |
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fragments = pd.read_csv(frag_path, sep='\t', header=None, |
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names=['chrom', 'start', 'end', 'source', 'score', 'strand']) |
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``` |
