Copy number prediction with correction for GC and mappability bias for HTS data

Bioconductor version: Release (2.11)

Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.

Author: Daniel Lai, Gavin Ha, Sohrab Shah

Maintainer: Daniel Lai <jujubix at>, Gavin Ha <gha at>, Sohrab Shah <sshah at>

To install this package, start R and enter:


To cite this package in a publication, start R and enter:



PDF R Script HMMcopy
PDF   Reference Manual


biocViews CopyNumberVariants, HighThroughputSequencing, Microarray, Preprocessing, Sequencing, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 2.11 (R-2.15)
License GPL-3
Depends R (>= 2.10.0), IRanges(>= 1.4.16), geneplotter(>= 1.24.0)
System Requirements
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source HMMcopy_1.0.0.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) HMMcopy_1.0.0.tgz
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center