ADaCGH2
Analysis of big data from aCGH experiments using parallel computing and ff objects
Bioconductor version: Release (3.20)
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 <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("ADaCGH2")):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
| ADaCGH2-long-examples.pdf | ||
| benchmarks.pdf | ||
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariants, Microarray, Software |
| Version | 2.46.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) (14 years) |
| License | GPL (>= 3) |
| Depends | R (>= 3.2.0), parallel, ff, GLAD |
| Imports | bit, DNAcopy, tilingArray, waveslim, cluster, aCGH |
| 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_2.46.0.tar.gz |
| Windows Binary (x86_64) | ADaCGH2_2.46.0.zip (64-bit only) |
| macOS Binary (x86_64) | ADaCGH2_2.46.0.tgz |
| macOS Binary (arm64) | ADaCGH2_2.46.0.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 |