CRAN

ABC.RAP 0.9.0

Array Based CpG Region Analysis Pipeline

Released Oct 20, 2016 by Abdulmonem Alsaleh

It aims to identify candidate genes that are “differentially methylated” between cases and controls. It applies Student’s t-test and delta beta analysis to identify candidate genes containing multiple “CpG sites”.

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>ABC.RAP</artifactId>
    <version>0.9.0-b15</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.cran:ABC.RAP')

Test Results

This package was last tested against Renjin 0.9.2644 on Jun 2, 2018.

• annotate_data-examples
• delta_beta_data-examples
• filter_data-examples
• plot_data-examples
• plot_gene-examples
• ttest_data-examples

Source

View GitHub Mirror

Release History

• 0.9.0