CancerMutationAnalysis

DOI: 10.18129/B9.bioc.CancerMutationAnalysis    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 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: 3.13

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 <smb310 at georgetown.edu>

Installation

To install this package, start R (version "4.1") 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

PDF		Reference Manual

Details

biocViews	Genetics, Software
Version	1.34.0
In Bioconductor since	BioC 2.10 (R-2.15) (9.5 years)
License	GPL (>= 2) + file LICENSE
Depends	R (>= 2.10.0), qvalue
Imports	AnnotationDbi, limma, methods, stats
LinkingTo
Suggests	KEGG.db
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Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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