source("http://bioconductor.org/biocLite.R")
biocLite("CancerMutationAnalysis")

CancerMutationAnalysis

Cancer mutation analysis

Bioconductor version: 2.13

This package implements gene and gene-set level analysis methods for somatic mutation studies of cancer. The gene-level methods distinguish between driver genes (which play an active role in tumorigenesis) and passenger genes (which are mutated in tumor samples, but have no role in tumorigenesis) and incorporate a two-stage study design. The gene-set methods implement a patient-oriented approach, which calculates gene-set scores for each sample, then combines them across samples; a gene-oriented approach which uses the Wilcoxon test is also provided for comparison.

Author: Giovanni Parmigiani, Simina M. Boca

Maintainer: Simina M. Boca <simina.boca at nih.gov>

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("CancerMutationAnalysis")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CancerMutationAnalysis")

 

PDF		CancerMutationAnalysisTutorial
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Bioinformatics, Genetics, Software
Version	1.6.0
In Bioconductor since	BioC 2.10 (R-2.15)
License	GPL (>= 2) + file LICENSE
Depends	R (>= 2.10.0), qvalue
Imports	AnnotationDbi, limma, methods, stats
Suggests	KEGG.db
System Requirements
URL
Depends On Me
Imports Me
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Package Archives

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

Package Source	CancerMutationAnalysis_1.6.0.tar.gz
Windows Binary	CancerMutationAnalysis_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	CancerMutationAnalysis_1.6.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats