CancerMutationAnalysis

This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CancerMutationAnalysis.

Cancer mutation analysis


Bioconductor version: 3.12

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 (version "4.0") and enter:


if (!require("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")
CancerMutationAnalysisTutorial PDF R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Genetics, Software
Version 1.32.0
In Bioconductor since BioC 2.10 (R-2.15) (12 years)
License GPL (>= 2) + file LICENSE
Depends R (>= 2.10.0), qvalue
Imports AnnotationDbi, limma, methods, stats
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Suggests KEGG.db
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Package Archives

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

Source Package CancerMutationAnalysis_1.32.0.tar.gz
Windows Binary CancerMutationAnalysis_1.32.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) CancerMutationAnalysis_1.32.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CancerMutationAnalysis
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CancerMutationAnalysis
Bioc Package Browser https://code.bioconductor.org/browse/CancerMutationAnalysis/
Package Short Url https://bioconductor.org/packages/CancerMutationAnalysis/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.12 Source Archive