ADaCGH2

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

Bioconductor version: 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 <rdiaz02 at gmail.com>, 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")

To cite this package in a publication, start R and enter:

    citation("ADaCGH2")

Documentation

PDF R Script ADaCGH2 Overview
PDF   Reference Manual

Details

biocViews Microarray, CopyNumberVariants
Depends R (>= 2.11.0), 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 1.2.0
Since Bioconductor 2.7 (R-2.12)

Package Downloads

Package Source ADaCGH2_1.2.0.tar.gz
Windows Binary ADaCGH2_1.2.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary ADaCGH2_1.2.0.tgz
Package Downloads Report Download Stats

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