CRAN
mutSignatures 1.2
Decipher Mutational Signatures from Somatic Mutational Catalogs
Released Jan 24, 2017 by Damiano Fantini
Dependencies
proxy 0.4-22 cluster 2.0.7-1 foreach 1.4.4 ggplot2 2.2.1 pracma 2.1.4 doParallel 1.0.11
Cancer cells accumulate DNA mutations as result of DNA damage and DNA repair processes. This computational framework is aimed at deciphering DNA mutational signatures operating in cancer. The input is a numeric matrix of DNA mutation counts detected in a panel of cancer samples. The framework performs Non-negative Matrix Factorization to extract the most likely signatures explaining the observed set of DNA mutations. The framework relies on parallelization and is optimized for use on multi-core systems. This framework is an R-based implementation of the original MATLAB WTSI framework by Alexandrov LB et al (2013)
Installation
Maven
This package can be included as a dependency from a Java or Scala project by including
the following your project's pom.xml file.
Read more
about embedding Renjin in JVM-based projects.
<dependencies>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>mutSignatures</artifactId>
<version>1.2-b22</version>
</dependency>
</dependencies>
<repositories>
<repository>
<id>bedatadriven</id>
<name>bedatadriven public repo</name>
<url>https://nexus.bedatadriven.com/content/groups/public/</url>
</repository>
</repositories>
Renjin CLI
If you're using Renjin from the command line, you load this library by invoking:
library('org.renjin.cran:mutSignatures')
Test Results
This package was last tested against Renjin 0.9.2644 on Jun 2, 2018.
- addWeak-examples
- bootstrapCancerGenomes-examples
- citation-examples
- do.nmf-examples
- evaluateStability-examples
- extractSignatures-examples
- filterOutIterations-examples
- getTestRunArgs-examples
- leadZeros-examples
- mutSignatures-package-examples
- plotSignatureExposures-examples
- removeWeak-examples
- setMutClusterParams-examples
- setMutCountObject-examples
- silhouetteMLB-examples