BioConductor

AtlasRDF 1.12.0

Gene Expression Atlas query and gene set enrichment package.

Released Jan 26, 2015 by James Malone, Simon Jupp, Maryam Soleimani

This package is available for Renjin and there are no known compatibility issues.

Dependencies

hash 3.0.1 SPARQL 1.16

Query the Gene Expression Atlas RDF data at the European Bioinformatics Institute using genes, experimental factors (such as disease, cell type, compound treatments), pathways and proteins. Also contains a function to perform an enrichment of your gene list across Experimental Factor Ontology (EFO) using the Atlas background set.

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>AtlasRDF</artifactId>
    <version>1.12.0-b3</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:AtlasRDF')

Test Results

This package was last tested against Renjin 0.8.2523 on Nov 12, 2017.

Source

R

Release History