source("http://bioconductor.org/biocLite.R")
biocLite("HMMcopy")

HMMcopy

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

Bioconductor version: 2.13

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 <jujubix at cs.ubc.ca>, Gavin Ha <gha at bccrc.ca>, Sohrab Shah <sshah at bccrc.ca>

Installation

To install this package, start R and enter:

source("http://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	CopyNumberVariants, HighThroughputSequencing, Microarray, Preprocessing, Sequencing, Software, Visualization
Version	1.4.0
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)
Imports
Suggests
System Requirements
URL
Depends On Me
Imports Me
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Package Archives

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

Package Source	HMMcopy_1.4.0.tar.gz
Windows Binary	HMMcopy_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	HMMcopy_1.4.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats