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 # Video files - compressed
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README.md

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----
-license: mit
----
+---
+license: mit
+task_categories:
+- tabular-regression
+tags:
+- biology
+- genomics
+pretty_name: "gReLU tutorial 3 dataset (Microglia scATAC-seq)"
+size_categories:
+- 10K<n<100K
+configs:
+- config_name: peaks
+  data_files:
+  - split: train
+    path: "peak_file.narrowPeak"
+- config_name: fragments
+  data_files:
+  - split: train
+    path: "fragment_file.bed"
+---
+
+# tutorial-3-data (Microglia scATAC pseudobulk)
+
+## 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 configurations: `peaks` and `fragments`.
+
+### 1. Peaks Configuration (`peak_file.narrowPeak`)
+Standard ENCODE narrowPeak format (tab-separated).
+- `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 Configuration (`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
+
+### Loading Peaks
+```python
+from datasets import load_dataset
+
+dataset = load_dataset("Genentech/tutorial-3-data", "peaks", split="train", delimiter="\t")
+dataset = load_dataset("Genentech/tutorial-3-data", "fragments", split="train", delimiter="\t")
+```

fragment_file.bed

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