CCLONE

This Github repository is complementary to our paper "Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data", which is out as preprint on Biorxiv.

Overview

This repository contains two sets of notebooks and a set of scripts:

• figure_notebooks/ contains all the notebooks to reproduce the analysis and figures in the paper
• tutorials/ shows and explains how to run the CCLONE analysis pipeline based on the example of patient P1 from the AML Smart-Seq2 dataset
• scrips/ the CCLONE package analysis starts from a anndata object with the REF and ALT count saved as layers. The scripts to generate such an object from a BAM file can be found here.

Requirements

The toolbox for CCLONE is available as a python package. This package, with additional information on installation can be found here.

References

Valérie Marot-Lassauzaie, et al. Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data bioRxiv (2024)

Support

If you found a bug, or have a question please open an issue.