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.

Versions 1.18.0, 1.20.0, 1.22.0
License GPL (>= 2) + file LICENSE
Links biotools: cancermutationanalysis, doi: 10.1007/978-1-62703-721-1_7


With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-cancermutationanalysis

and update with:

conda update bioconductor-cancermutationanalysis


A Docker container is available at