rCGH

Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

Bioconductor version: Release (3.17)

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 (from within R, enter citation("rCGH")):

Installation

To install this package, start R (version "4.3") 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	PDF	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	CopyNumberVariation, FeatureExtraction, Preprocessing, Software, aCGH
Version	1.30.0
In Bioconductor since	BioC 3.2 (R-3.2) (8 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
Linking To
Suggests	BiocStyle, knitr, BiocGenerics, RUnit
System Requirements
Enhances
URL	https://github.com/fredcommo/rCGH

Depends On Me
Imports Me	preciseTAD
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	rCGH_1.30.0.tar.gz
Windows Binary	rCGH_1.30.0.zip
macOS Binary (x86_64)	rCGH_1.30.0.tgz
macOS Binary (arm64)	rCGH_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rCGH
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rCGH
Bioc Package Browser	https://code.bioconductor.org/browse/rCGH/
Package Short Url	https://bioconductor.org/packages/rCGH/
Package Downloads Report	Download Stats