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ADaCGH2

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


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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")
ADaCGH2 Overview PDF R Script
ADaCGH2-long-examples.pdf PDF
benchmarks.pdf PDF
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariants, Microarray, Software
Version 2.42.0
In Bioconductor since BioC 2.7 (R-2.12) (13.5 years)
License GPL (>= 3)
Depends R (>= 3.2.0), parallel, ff, GLAD
Imports bit, DNAcopy, tilingArray, waveslim, cluster, aCGH, snapCGH
System Requirements
URL https://github.com/rdiaz02/adacgh2
See More
Suggests CGHregions, Cairo, limma
Linking To
Enhances Rmpi
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package ADaCGH2_2.42.0.tar.gz
Windows Binary ADaCGH2_2.42.0.zip (64-bit only)
macOS Binary (x86_64) ADaCGH2_2.42.0.tgz
macOS Binary (arm64) ADaCGH2_2.42.0.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