ADaCGH2

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

Bioconductor version: Development (2.8)

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.

Author: Ramon Diaz-Uriarte, Oscar M. Rueda . Wavelet-based aCGH smoothing code from Li Hsu and Douglas Grove . Imagemap code from Barry Rowlingson . HaarSeg code from Erez Ben-Yaacov; downloaded from

Maintainer: Ramon Diaz-Uriarte

To install this package, start R and enter:

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

Documentation

PDF R Script ADaCGH2 Overview

Reference Manual

Details

biocViews Microarray, CopyNumberVariants
Depends R, tilingArray, aCGH, waveslim, cluster, snapCGH, snowfall, ff
Imports
Suggests GLAD, DNAcopy, CGHregions, rlecuyer
System Requirements
License GPL (>= 3)
URL http://launchpad.net/adacgh, http://wavicgh.bioinfo.cnio.es
Depends On Me
Imports Me
Suggests Me
Version 1.1.1

Package Downloads

Package Source ADaCGH2_1.1.1.tar.gz
Windows Binary ADaCGH2_1.1.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary ADaCGH2_1.1.1.tgz
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