DOI: 10.18129/B9.bioc.CancerMutationAnalysis    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see CancerMutationAnalysis.

Cancer mutation analysis

Bioconductor version: 3.10

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 <smb310 at>

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


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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PDF R Script CancerMutationAnalysisTutorial
PDF   Reference Manual
Text   NEWS


biocViews Genetics, Software
Version 1.28.0
In Bioconductor since BioC 2.10 (R-2.15) (8 years)
License GPL (>= 2) + file LICENSE
Depends R (>= 2.10.0), qvalue
Imports AnnotationDbi, limma, methods, stats
Suggests KEGG.db
Depends On Me
Imports Me
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