|
|
--- |
|
|
|
|
|
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/binary-atac-tutorial-data", |
|
|
repo_type="dataset", |
|
|
filename="data.h5ad" |
|
|
) |
|
|
ad = anndata.read_h5ad(file_path) |
|
|
``` |
