ASTER is available on PyPI here and can be installed via
pip install epiaster
You can also install ASTER from GitHub via
git clone git://github.com/BioX-NKU/ASTER.git
cd ASTER
python setup.py install
The dependencies will be automatically installed along with ASTER.
- adata: AnnData object of shape
n_obs
×n_vars
. Rows correspond to cells and columns to genes. - search_list: List of optional numbers of cell types for the estimation.
- estimated_k: Estimated number of cell types.
ASTER can also be seamlessly integrated with EpiScanpy, a widely-used Python library for epigenomics single cell analysis:
import episcanpy.api as epi
import epiaster as aster
# Load the single-cell chromatin accessibility data as an AnnData object (adata)
# Run ASTER
estimated_k = aster.estimate_k(adata, search_list)