CancerMutationAnalysis

Cancer mutation analysis

Bioconductor version: 2.10

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("CancerMutationAnalysis")

Documentation

PDF R Script CancerMutationAnalysisTutorial
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Software
Depends R (>= 2.10.0), qvalue
Imports AnnotationDbi, limma, methods, stats
Suggests KEGG.db
System Requirements
License GPL (>= 2) + file LICENSE
URL
Depends On Me
Imports Me
Suggests Me
Version 1.0.0
Since Bioconductor 2.10 (R-2.15)

Package Downloads

Package Source CancerMutationAnalysis_1.0.0.tar.gz
Windows Binary CancerMutationAnalysis_1.0.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary CancerMutationAnalysis_1.0.0.tgz
Package Downloads Report Download Stats

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Fred Hutchinson Cancer Research Center