aCGH
This is the released version of aCGH; for the devel version, see aCGH.
Classes and functions for Array Comparative Genomic Hybridization data
Bioconductor version: Release (3.23)
Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.
Author: Jane Fridlyand <jfridlyand at cc.ucsf.edu>, Peter Dimitrov <dimitrov at stat.Berkeley.EDU>
Maintainer: Peter Dimitrov <dimitrov at stat.Berkeley.EDU>
citation("aCGH")):
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("aCGH")
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("aCGH")| aCGH Overview | R Script | |
| Reference Manual |
Details
| biocViews | CopyNumberVariation, DataImport, Genetics, Software |
| Version | 1.90.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | GPL-2 |
| Depends | R (>= 2.10), cluster, survival, multtest |
| Imports | Biobase, grDevices, graphics, methods, stats, splines, utils |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | CRImage |
| Imports Me | ADaCGH2 |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | aCGH_1.90.0.tar.gz |
| Windows Binary (x86_64) | aCGH_1.90.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | aCGH_1.90.0.tgz |
| macOS Binary (sonoma-arm64) | aCGH_1.90.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/aCGH |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/aCGH |
| Bioc Package Browser | https://code.bioconductor.org/browse/aCGH/ |
| Package Short Url | https://bioconductor.org/packages/aCGH/ |
| Package Downloads Report | Download Stats |