CancerMutationAnalysis

DOI: 10.18129/B9.bioc.CancerMutationAnalysis    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see CancerMutationAnalysis.

Cancer mutation analysis

Bioconductor version: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("CancerMutationAnalysis")

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("CancerMutationAnalysis")

 

PDF	R Script	CancerMutationAnalysisTutorial
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Genetics, Software
Version	1.30.0
In Bioconductor since	BioC 2.10 (R-2.15) (8.5 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
Links To Me
Build Report

Package Archives

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

Source Package	CancerMutationAnalysis_1.30.0.tar.gz
Windows Binary	CancerMutationAnalysis_1.30.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	CancerMutationAnalysis_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CancerMutationAnalysis
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CancerMutationAnalysis
Package Short Url	https://bioconductor.org/packages/CancerMutationAnalysis/
Package Downloads Report	Download Stats