CHAT: Clonal Heterogeneity Analysis Tool

CHAT is a collection of tools developed for tumor subclonality analysis using high density DNA SNP array data and sequencing data. The pipeline consists of four major compartments: 1) tumor aneuploid genome proportion (AGP) calculation and ploidy estimation. 2) segment-specific AGP calculation and absolute copy number estimation for somatic CNAs. 3) cancer cell fraction correction for somatic SNVs in clonal or subclonal sCNA regions. 4) number of subclones estimation using Dirichlet process prior followed by MCMC approach.

Version: 1.1
Depends: R (≥ 2.10), parallel, DNAcopy, DPpackage
Published: 2014-08-09
Author: Bo Li
Maintainer: Bo Li <libo at umich.edu>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: http://sourceforge.net/p/clonalhetanalysistool/wiki/CHAT/
NeedsCompilation: no
CRAN checks: CHAT results

Downloads:

Reference manual: CHAT.pdf
Package source: CHAT_1.1.tar.gz
Windows binaries: r-devel: CHAT_1.1.zip, r-release: CHAT_1.1.zip, r-oldrel: CHAT_1.1.zip
OS X El Capitan binaries: r-release: CHAT_1.1.tgz
OS X Mavericks binaries: r-oldrel: CHAT_1.1.tgz
Old sources: CHAT archive

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