To install this package, start R and enter:

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

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

ADaCGH2

 

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

Bioconductor version: Release (3.1)

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>

Citation (from within R, enter citation("ADaCGH2")):

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 ADaCGH2-long-examples.pdf
PDF benchmarks.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumberVariants, Microarray, Software
Version 2.8.1
In Bioconductor since BioC 2.7 (R-2.12) (5 years)
License GPL (>= 3)
Depends R (>= 2.15.0), parallel, ff
Imports bit, ffbase, DNAcopy, tilingArray, GLAD, waveslim, cluster, aCGH, snapCGH
LinkingTo
Suggests CGHregions, Cairo, limma
SystemRequirements
Enhances Rmpi
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source ADaCGH2_2.8.1.tar.gz
Windows Binary ADaCGH2_2.8.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ADaCGH2_2.8.1.tgz
Mac OS X 10.9 (Mavericks) ADaCGH2_2.8.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ADaCGH2/tree/release-3.1
Package Short Url http://bioconductor.org/packages/ADaCGH2/
Package Downloads Report Download Stats

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