This package provides functions for analyis of single-cell variant call data. We introduce CCLONE based on a weighted NMF.
The tools in this package are compatible with scanpy.
To install the package from GitHub, please use:
git clone https://github.com/HaghverdiLab/CCLONE
cd CCLONE
pip install -e .
CCLONE takes as input an Anndata object with REF and ALT count matrices for variants saved in the Anndata.layers.
Tutorials explaining the analysis workflow with CCLONE can be found here, scripts to convert cellsnp-lite output to the needed Anndata object can also be found there.
Valérie Marot-Lassauzaie, et al.
If you found a bug, would like to see a feature implemented, or have a question please open an issue.