ADaCGH2

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

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

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

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

Documentation

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

Details

biocViews CopyNumberVariation, Microarray, Software
Version 2.4.0
In Bioconductor since BioC 2.7 (R-2.12)
License GPL (>= 3)
Depends R (>= 2.15.0), parallel, ff
Imports bit, ffbase, DNAcopy, tilingArray, GLAD, waveslim, cluster, aCGH, snapCGH
Suggests CGHregions, Cairo, limma
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source ADaCGH2_2.4.0.tar.gz
Windows Binary ADaCGH2_2.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ADaCGH2_2.4.0.tgz
Mac OS X 10.9 (Mavericks) ADaCGH2_2.4.0.tgz
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