HMMcopy

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see HMMcopy.

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


Bioconductor version: 3.13

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 bccrc.ca>, Sohrab Shah <shahs3 at mskcc.org>

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

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HMMcopy")

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

Documentation

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

browseVignettes("HMMcopy")
HMMcopy PDF R Script
Reference Manual PDF

Details

biocViews CopyNumberVariation, Microarray, Preprocessing, Sequencing, Software, Visualization
Version 1.34.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License GPL-3
Depends R (>= 2.10.0), data.table (>= 1.11.8)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HMMcopy_1.34.0.tar.gz
Windows Binary HMMcopy_1.34.0.zip
macOS 10.13 (High Sierra) HMMcopy_1.34.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/HMMcopy
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HMMcopy
Bioc Package Browser https://code.bioconductor.org/browse/HMMcopy/
Package Short Url https://bioconductor.org/packages/HMMcopy/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive