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
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see rCGH.
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
Bioconductor version: 3.3
A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data is in a suitable format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to segmenting and annotating genes. This package provides several visualization functions (static or interactive) which facilitate individual 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")
| R Script | using rCGH package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, FeatureExtraction, Preprocessing, Software, aCGH |
| Version | 1.2.2 |
| In Bioconductor since | BioC 3.2 (R-3.2) (1 year) |
| License | Artistic-2.0 |
| Depends | R (>= 3.2.1), methods, stats, utils, graphics |
| Imports | plyr, DNAcopy, lattice, ggplot2, grid, shiny (>= 0.11.1), limma, affy, mclust, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, GenomicFeatures, GenomeInfoDb, GenomicRanges, AnnotationDbi, parallel, IRanges, grDevices, aCGH |
| 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_1.2.2.tar.gz |
| Windows Binary | rCGH_1.2.2.zip |
| Mac OS X 10.9 (Mavericks) | rCGH_1.2.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/rCGH/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/rCGH/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
