ADaCGH2

This is the released version of ADaCGH2; for the devel version, see ADaCGH2.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7

Analysis of Big Data from aCGH Experiments using Parallel Computing and ff Objects

Bioconductor version: Release (3.23)

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, 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 [aut, cre] ORCID: 0000-0002-6637-9039 , Oscar M. Rueda [aut], Li Hsu [ctb] (Wavelet-based aCGH smoothing code), Douglas Grove [ctb] (Wavelet-based aCGH smoothing code), Barry Rowlingson [ctb] (Imagemap code), Erez Ben-Yaacov [ctb] (HaarSeg code), Edwin de Jonge [ctb] (Code from ffbase), Jan Wijffels [ctb] (Code from ffbase), Jan van der Laan [ctb] (Code from ffbase)

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

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

Ramon Diaz-Uriarte, Oscar M. Rueda. ADaCGH2: Analysis of Big Data from aCGH Experiments using Parallel Computing and ff Objects. doi:10.18129/B9.bioc.ADaCGH2, R package version 2.52.0, https://bioconductor.org/packages/ADaCGH2.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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-long-examples.pdf	PDF
ADaCGH2 Overview	PDF	R Script
benchmarks.pdf	PDF
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, Microarray, Software, aCGH
Version	2.52.0
In Bioconductor since	BioC 2.7 (R-2.12) (16 years)
License	GPL (>= 3)
Depends	R (>= 3.2.0), parallel, ff
Imports	bit, DNAcopy, tilingArray, waveslim, cluster, aCGH
System Requirements
URL	https://github.com/rdiaz02/adacgh2
Bug Reports	https://github.com/rdiaz02/adacgh2

Suggests	CGHregions, Cairo, limma
Linking To
Enhances	Rmpi, GLAD
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	ADaCGH2_2.52.0.tar.gz
Windows Binary (x86_64)	ADaCGH2_2.52.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	ADaCGH2_2.52.0.tgz
macOS Binary (sonoma-arm64)	ADaCGH2_2.52.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ADaCGH2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ADaCGH2
Package Short Url	https://bioconductor.org/packages/ADaCGH2/
Package Downloads Report	Download Stats