xcltk: Toolkit for XClone Preprocessing

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

News

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

All release notes are available at docs/release.rst

Installation

Install via pip (latest stable version)

xcltk is avaliable through pypi.

pip install -U xcltk

Install from this Github Repo (latest stable/dev version)

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.

Manual

You can check the full parameters with xcltk -h.

Program: xcltk (Toolkit for XClone Preprocessing)
Version: 0.5.2

Usage:   xcltk <command> [options]

Commands:
  -- BAF calculation
     baf              Preprocessing pipeline for XClone BAF.
     fixref           Fix REF allele mismatches based on reference FASTA.

  -- 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.