xcltk - Toolkit for XClone
Project description
xcltk: Toolkit for XClone Preprocessing
XClone is a statistical method to detect haplotype-aware 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.
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
xcltk is avaliable through pypi.
To install, type the following command line, and add -U
for upgrading:
pip install -U xcltk
Alternatively, you can install from this GitHub repository for latest (often development) version by following command line
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: 0.3.0
Usage: xcltk <command> [options]
Commands:
-- BAF calculation
allelefc Allele counting for each feature.
baf Preprocessing pipeline for XClone BAF.
fixref Fix REF, ALT and GT.
rpc Reference phasing correction.
-- RDR calculation
basefc Basic feature counting.
-- Tools
convert Convert different region file formats.
-- Others
-h, --help Print this message and exit.
-V, --version Print version and exit.
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