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

Bioconductor version: Release (3.19)

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 <dalai at>

Citation (from within R, enter citation("HMMcopy")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

HMMcopy PDF R Script
Reference Manual PDF


biocViews CopyNumberVariation, Microarray, Preprocessing, Sequencing, Software, Visualization
Version 1.46.0
In Bioconductor since BioC 2.11 (R-2.15) (12 years)
License GPL-3
Depends R (>= 2.10.0), data.table (>= 1.11.8)
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Follow Installation instructions to use this package in your R session.

Source Package HMMcopy_1.46.0.tar.gz
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macOS Binary (x86_64) HMMcopy_1.46.0.tgz
macOS Binary (arm64) HMMcopy_1.46.0.tgz
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