BioConductor

GeneRegionScan 1.36.0

GeneRegionScan

Released Oct 16, 2009 by Lasse Folkersen

This package can be loaded by Renjin but 10 out 12 tests failed.

Dependencies

RColorBrewer 1.1-2 Biobase 2.40.0 affxparser 1.52.0 S4Vectors 0.18.3 Biostrings 2.48.0

A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.

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.bioconductor</groupId>
    <artifactId>GeneRegionScan</artifactId>
    <version>1.36.0-b2</version>
  </dependency>
</dependencies>
<repositories>
  <repository>
    <id>bedatadriven</id>
    <name>bedatadriven public repo</name>
    <url>https://nexus.bedatadriven.com/content/groups/public/</url>
  </repository>
</repositories>

View build log

Renjin CLI

If you're using Renjin from the command line, you load this library by invoking:

library('org.renjin.bioconductor:GeneRegionScan')

Test Results

This package was last tested against Renjin 0.9.2687 on Aug 25, 2018.