XClone is a statistical method to detect allele- and haplotype-specific copy number variations (CNVs) and reconstruct tumour clonal substructure from scRNA-seq data, by integrating the expression levels (read depth ratio; RDR signals) and the allelic balance (B-allele frequency; BAF signals). It takes three matrices as input: the allele-specific AD and DP matrices (BAF signals) and the total read depth matrix (RDR signals).

The xcltk package implements a preprocessing pipeline to generate the three matrices from SAM/BAM/CRAM files. It supports data from multiple single-cell sequencing platforms, including droplet-based (e.g., 10x Genomics) and well-based (e.g., SMART-seq) platforms.

For details of xcltk and XClone, please checkout our paper:

Huang, R., Huang, X., Tong, Y. et al. Robust analysis of allele-specific copy number alterations from scRNA-seq data with XClone. Nat Commun 15, 6684 (2024). https://doi.org/10.1038/s41467-024-51026-0

You can find the full manual of the xcltk preprocessing pipeline at preprocess/README.md.

All release notes are available at docs/release.rst

xcltk is avaliable through pypi.

pip install -U xcltk

pip install -U git+https://github.com/hxj5/xcltk

In either case, if you don't have write permission for your current Python environment, we suggest creating a separate conda environment or add --user for your current one.

You can check the full parameters with xcltk -h.

Program: xcltk (Toolkit for XClone Preprocessing) Version: 0.4.1 Usage: xcltk <command> [options] Commands: -- BAF calculation allelefc Allele-specific feature counting. baf Preprocessing pipeline for XClone BAF. fixref Fix REF allele mismatches based on reference FASTA. rpc Reference phasing correction. -- RDR calculation basefc Basic feature counting. -- Tools convert Convert between different formats of genomic features. -- Others -h, --help Print this message and exit. -V, --version Print version and exit.