CRAN
aBioMarVsuit 1.0
A Biomarker Validation Suit for predicting Survival using gene signature.
Released Jan 15, 2013 by Pushpike Thalikarathne
Dependencies
superpc 1.09 DLBCL 1.16.0 gplots 2.11.0 pls 2.3-0 glmnet 1.8-5 survival 2.37-2 Biobase 2.28.0
This package is useful in finding and validating predictive gene signature for classifying low risk versus high risk patients in early phase clinical trials. The primary end point is survival, and classification of cancer patients into low risk or high risk groups is mainly based on median cutoff, but others can be considered as well. It can also accommodate the prognostic factors if any. Both statistical and machine learning techniques are integrated as validating suit. The package can be used to perform the analysis using the entire samples and can also be used to carryout large scale cross validations. For the first instance, package reduces larger gene expression matrix to smaller version using supervised principle components analysis. Later entire validation procedure can be performed using reduced gene expression matrix with various types of validation schemes.
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>aBioMarVsuit</artifactId>
<version>1.0-b228</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:aBioMarVsuit')
Test Results
This package was last tested against Renjin 0.8.2500 on Oct 28, 2017.