ADaCGH2

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

Bioconductor version: Release (2.7)

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	1.0.0

Package Downloads

Package Source	ADaCGH2_1.0.0.tar.gz
Windows Binary	ADaCGH2_1.0.0.zip (32-bit only)
MacOS 10.5 (Leopard) binary	ADaCGH2_1.0.0.tgz
Package Downloads Report	Download Stats