rCGH
This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see rCGH.
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
Bioconductor version: 3.6
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 complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also 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 <fredcommo at gmail.com>
citation("rCGH")):
Installation
To install this package, start R (version "3.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rCGH")
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("rCGH")| using rCGH package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, FeatureExtraction, Preprocessing, Software, aCGH |
| Version | 1.8.1 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.4), 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 |
| System Requirements | |
| URL | https://github.com/fredcommo/rCGH |
See More
| Suggests | BiocStyle, knitr, BiocGenerics, RUnit |
| Linking To | |
| Enhances | |
| 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 | rCGH_1.8.1.tar.gz |
| Windows Binary | rCGH_1.8.1.zip |
| Mac OS X 10.11 (El Capitan) | rCGH_1.8.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/rCGH |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rCGH |
| Package Short Url | https://bioconductor.org/packages/rCGH/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |