| # 1. Metadata Block | |
| license: mit | |
| task_categories: | |
| - tabular-classification | |
| tags: | |
| - biology | |
| - genomics | |
| pretty_name: "gReLU Tutorial 2 dataset" | |
| size_categories: | |
| - 1M<n<10M | |
| # tutorial-2-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", filename="data.h5ad") | |
| ada = anndata.read_h5ad(file_path) | |
| ``` |