To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CancerMutationAnalysis")

In most cases, you don't need to download the package archive at all.

CancerMutationAnalysis

 

   

This is the development version of CancerMutationAnalysis; for the stable release version, see CancerMutationAnalysis.

Cancer mutation analysis

Bioconductor version: Development (3.4)

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 <smb310 at georgetown.edu>

Citation (from within R, enter citation("CancerMutationAnalysis")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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 R Script CancerMutationAnalysisTutorial
PDF   Reference Manual

Details

biocViews Genetics, Software
Version 1.15.0
In Bioconductor since BioC 2.10 (R-2.15) (4.5 years)
License GPL (>= 2) + file LICENSE
Depends R (>= 2.10.0), qvalue
Imports AnnotationDbi, limma, methods, stats
LinkingTo
Suggests KEGG.db
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source CancerMutationAnalysis_1.15.0.tar.gz
Windows Binary CancerMutationAnalysis_1.15.0.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) CancerMutationAnalysis_1.15.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/CancerMutationAnalysis
Package Short Url http://bioconductor.org/packages/CancerMutationAnalysis/
Package Downloads Report Download Stats

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