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CancerMutationAnalysis

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.

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CancerMutationAnalysis classification

CancerMutationAnalysis specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
1.0
Requirements:
qvalue

CancerMutationAnalysis distribution

versioning

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No versioning.

CancerMutationAnalysis support

Documentation

Maintainer

  • Simina M. Boca <>

Credits

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Publications

Institution(s)

Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA

Link to literature

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