| --- |
| |
| license: mit |
| task_categories: |
| - tabular-classification |
| tags: |
| - biology |
| - genomics |
| pretty_name: "gReLU Tutorial 2 dataset" |
| size_categories: |
| - 1M<n<10M |
| --- |
| |
| # binary-atac-tutorial-data |
|
|
| ## Dataset Summary |
| This dataset contains binary accessibility values for 1154611 CREs in 222 cell types. The original source of this data is CATlas (https://decoder-genetics.wustl.edu/catlasv1/humanenhancer/data/cCRE_by_cell_type/). For more details, see https://decoder-genetics.wustl.edu/catlasv1/catlas_humanenhancer/#!/. This version of the dataset is used in gReLU tutorial 2 (https://github.com/Genentech/gReLU/blob/main/docs/tutorials/2_finetune.ipynb). |
| |
| ## Dataset Structure |
| |
| ### Data Fields |
| In `.obs`: |
| |
| | Column | Type | Description | |
| | :--- | :--- | :--- | |
| | `cell type` | string | Name of the cell type | |
| |
| In `.var`: |
| |
| | Column | Type | Description | |
| | :--- | :--- | :--- | |
| | `chrom` | string | Chromosome (e.g., `chr6`) | |
| | `start` | int | Genomic start position (hg38) | |
| | `end` | int | Genomic end position (hg38) | |
| | `Class` | category | CRE class | |
| |
| `.X` is a binary accessibility matrix of shape (222 × 1154611) in Compressed Sparse Row format. |
| |
| ## Usage |
| |
| ```python |
| import anndata |
| from huggingface_hub import hf_hub_download |
|
|
| file_path = hf_hub_download( |
| repo_id="Genentech/tutorial-2-data", |
| repo_type="dataset", |
| filename="data.h5ad" |
| ) |
| ad = anndata.read_h5ad(file_path) |
| ``` |
