source("http://bioconductor.org/biocLite.R")
biocLite("ADaCGH2")

ADaCGH2

Analysis of big data from aCGH experiments using parallel computing and ff objects

Bioconductor version: 2.13

Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.

Author: Ramon Diaz-Uriarte <rdiaz02 at gmail.com> and Oscar M. Rueda <rueda.om at gmail.com>. Wavelet-based aCGH smoothing code from Li Hsu <lih at fhcrc.org> and Douglas Grove <dgrove at fhcrc.org>. Imagemap code from Barry Rowlingson <B.Rowlingson at lancaster.ac.uk>. HaarSeg code from Erez Ben-Yaacov; downloaded from <http://www.ee.technion.ac.il/people/YoninaEldar/Info/software/HaarSeg.htm>

Maintainer: Ramon Diaz-Uriarte <rdiaz02 at gmail.com>

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("ADaCGH2")

Documentation

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

browseVignettes("ADaCGH2")

 

PDF	R Script	ADaCGH2 Overview
PDF	R Script	ADaCGH2-long-examples.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariants, Microarray, Software
Version	2.2.0
In Bioconductor since	BioC 2.7 (R-2.12)
License	GPL (>= 3)
Depends	R (>= 2.15.0), parallel, ff
Imports	bit, ffbase, DNAcopy, snapCGH, tilingArray, aCGH, GLAD, waveslim, cluster
Suggests	CGHregions, Cairo, limma
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	ADaCGH2_2.2.0.tar.gz
Windows Binary	ADaCGH2_2.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	ADaCGH2_2.2.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats