To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("HMMcopy")

In most cases, you don't need to download the package archive at all.

HMMcopy

This package is for version 3.4 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: 3.4

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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("HMMcopy")

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 1.16.0
In Bioconductor since BioC 2.11 (R-2.15) (4.5 years)
License GPL-3
Depends R (>= 2.10.0), IRanges(>= 1.4.16), geneplotter(>= 1.24.0)
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me qsea
Suggests Me
Build Report

Package Archives

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

Package Source HMMcopy_1.16.0.tar.gz
Windows Binary HMMcopy_1.16.0.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) HMMcopy_1.16.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/HMMcopy/tree/release-3.4
Package Short Url http://bioconductor.org/packages/HMMcopy/
Package Downloads Report Download Stats

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