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 is the development version of ADaCGH2; for the stable release version, see ADaCGH2.

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

Bioconductor version: Development (3.4)

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>

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

Details

biocViews CopyNumberVariants, Microarray, Software
Version 2.13.0
In Bioconductor since BioC 2.7 (R-2.12) (6 years)
License GPL (>= 3)
Depends R (>= 3.2.0), parallel, ff, GLAD
Imports bit, ffbase, DNAcopy, tilingArray, waveslim, cluster, aCGH, snapCGH
LinkingTo
Suggests CGHregions, Cairo, limma
SystemRequirements
Enhances Rmpi
URL https://github.com/rdiaz02/adacgh2
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_2.13.0.tar.gz
Windows Binary ADaCGH2_2.13.0.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) ADaCGH2_2.13.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ADaCGH2
Package Short Url http://bioconductor.org/packages/ADaCGH2/
Package Downloads Report Download Stats

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