To install this package, start R and enter:

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

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

HMMcopy

This is the development version of HMMcopy; for the stable release version, see HMMcopy.

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

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

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

Installation

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 CopyNumberVariation, Microarray, Preprocessing, Sequencing, Software, Visualization
Version 1.7.0
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
Suggests Me

Package Archives

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

Package Source HMMcopy_1.7.0.tar.gz
Windows Binary HMMcopy_1.7.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) HMMcopy_1.7.0.tgz
Mac OS X 10.9 (Mavericks) HMMcopy_1.7.0.tgz
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center