To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rCGH")
In most cases, you don't need to download the package archive at all.
rCGH
|
Comprehensive Pipeline for Analyzing and Visualizing Agilent and Affymetrix Array-Based CGH Data
Bioconductor version: 3.2
A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through Agilent and Affymetrix microarrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, and Affymetrix SNP6.0 and cytoScan probeset.txt, cychp.txt, and cnchp.txt files, exported from ChAS or Affymetrix Power Tools. This package takes over all the steps required for a genomic profile analysis, from reading the files to the segmentation and genes annotations, and provides several visualization functions (static or interactive) which facilitate profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.
Author: Frederic Commo [aut, cre]
Maintainer: Frederic Commo <frederic.commo at gustaveroussy.fr>
Citation (from within R,
enter citation("rCGH")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rCGH")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rCGH")
| using rCGH package | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, FeatureExtraction, Preprocessing, Software, aCGH |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.2 (R-3.2) (0.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.2.1), methods |
| Imports | plyr, DNAcopy, lattice, aCGH, ggplot2, grid, shiny (>= 0.11.1), limma, affy, mclust, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, GenomicFeatures, GenomeInfoDb, GenomicRanges, AnnotationDbi, parallel, stats, utils, graphics, IRanges, grDevices |
| LinkingTo | |
| Suggests | BiocStyle, knitr, BiocGenerics, RUnit |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/fredcommo/rCGH |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | rCGH_1.0.2.tar.gz |
| Windows Binary | rCGH_1.0.2.zip |
| Mac OS X 10.6 (Snow Leopard) | rCGH_1.0.2.tgz |
| Mac OS X 10.9 (Mavericks) | rCGH_1.0.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/rCGH/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/rCGH/ |
| Package Downloads Report | Download Stats |
Documentation »
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