ADaCGH2

DOI: 10.18129/B9.bioc.ADaCGH2  

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

Bioconductor version: Release (3.16)

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>. Code from ffbase <https://github.com/edwindj/ffbase> by Edwin de Jonge <edwindjonge at gmail.com>, Jan Wijffels, Jan van der Laan.

Maintainer: Ramon Diaz-Uriarte <rdiaz02 at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ADaCGH2")

For older versions of R, please refer to the appropriate Bioconductor release.

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
Text		NEWS

Details

biocViews	CopyNumberVariants, Microarray, Software
Version	2.38.0
In Bioconductor since	BioC 2.7 (R-2.12) (12.5 years)
License	GPL (>= 3)
Depends	R (>= 3.2.0), parallel, ff, GLAD
Imports	bit, 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
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ADaCGH2_2.38.0.tar.gz
Windows Binary	ADaCGH2_2.38.0.zip (64-bit only)
macOS Binary (x86_64)	ADaCGH2_2.38.0.tgz
macOS Binary (arm64)	ADaCGH2_2.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ADaCGH2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ADaCGH2
Bioc Package Browser	https://code.bioconductor.org/browse/ADaCGH2/
Package Short Url	https://bioconductor.org/packages/ADaCGH2/
Package Downloads Report	Download Stats