HMMcopy

DOI: 10.18129/B9.bioc.HMMcopy    

This package is for version 3.9 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: 3.9

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 <sshah at bccrc.ca>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	HMMcopy
PDF		Reference Manual

Details

biocViews	CopyNumberVariation, Microarray, Preprocessing, Sequencing, Software, Visualization
Version	1.26.0
In Bioconductor since	BioC 2.11 (R-2.15) (7 years)
License	GPL-3
Depends	R (>= 2.10.0), IRanges(>= 1.4.16), geneplotter(>= 1.24.0)
Imports
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Depends On Me
Imports Me	qsea
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Build Report

Package Archives

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

Source Package	HMMcopy_1.26.0.tar.gz
Windows Binary	HMMcopy_1.26.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	HMMcopy_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HMMcopy
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HMMcopy
Package Short Url	https://bioconductor.org/packages/HMMcopy/
Package Downloads Report	Download Stats