ADaCGH2
This is the released version of ADaCGH2; for the devel version, see ADaCGH2.
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]
, 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("ADaCGH2")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 Overview | R Script | |
| ADaCGH2-long-examples.pdf | ||
| benchmarks.pdf | ||
| Reference Manual | ||
| NEWS | Text |
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 |
See More
| Suggests | CGHregions, Cairo, limma |
| Linking To | |
| Enhances | Rmpi, GLAD |
| 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_2.52.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/ADaCGH2/ |
| Package Short Url | https://bioconductor.org/packages/ADaCGH2/ |
| Package Downloads Report | Download Stats |