CGHcall

DOI: 10.18129/B9.bioc.CGHcall    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CGHcall.

Calling aberrations for array CGH tumor profiles.

Bioconductor version: 3.9

Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.

Author: Mark van de Wiel, Sjoerd Vosse

Maintainer: Mark van de Wiel <mark.vdwiel at vumc.nl>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CGHcall")

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("CGHcall")

 

PDF	R Script	CGHcall
PDF		Reference Manual

Details

biocViews	Microarray, Preprocessing, Software, Visualization
Version	2.46.0
In Bioconductor since	BioC 2.1 (R-2.6) (12 years)
License	GPL (http://www.gnu.org/copyleft/gpl.html)
Depends	R (>= 2.0.0), impute(>= 1.8.0), DNAcopy(>= 1.6.0), methods, Biobase, CGHbase(>= 1.15.1), snowfall
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me	CGHnormaliter, focalCall, GeneBreak
Imports Me	CGHnormaliter, QDNAseq
Suggests Me	sigaR
Links To Me
Build Report

Package Archives

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

Source Package	CGHcall_2.46.0.tar.gz
Windows Binary	CGHcall_2.46.0.zip
Mac OS X 10.11 (El Capitan)	CGHcall_2.46.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CGHcall
Source Repository (Developer Access)	git clone [email protected]:packages/CGHcall
Package Short Url	https://bioconductor.org/packages/CGHcall/
Package Downloads Report	Download Stats