To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ADaCGH2")

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

ADaCGH2

   

This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see 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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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 ADaCGH2.pdf
PDF   Reference Manual

Details

biocViews CopyNumberVariants, Microarray, Software
Version 1.2.0
In Bioconductor since BioC 2.7 (R-2.12) (5.5 years)
License GPL (>= 3)
Depends R (>= 2.11.0), tilingArray, aCGH, waveslim, cluster, snapCGH, snowfall, ff
Imports
LinkingTo
Suggests GLAD, DNAcopy, CGHregions, rlecuyer
SystemRequirements
Enhances Rmpi, multicore
URL http://launchpad.net/adacgh http://wavicgh.bioinfo.cnio.es
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_1.2.0.tar.gz
Windows Binary ADaCGH2_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ADaCGH2/tree/release-2.8
Package Short Url http://bioconductor.org/packages/ADaCGH2/
Package Downloads Report Download Stats

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