BioConductor

ALDEx2 1.8.0

Analysis Of Differential Abundance Taking Sample Variation Into Account

Released Jul 27, 2016 by Greg Gloor, Ruth Grace Wong, Andrew Fernandes, Arianne Albert, Matt Links, Jia Rong Wu

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

Dependencies

GenomicRanges 1.28.6 S4Vectors 0.14.7 BiocParallel 1.10.1 IRanges 2.10.5 SummarizedExperiment 1.6.5

A differential abundance analysis for the comparison of two or more conditions. For example, single-organism and meta-RNA-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected false discovery rate given the biological and sampling variation using the Wilcox rank test or Welches t-test (aldex.ttest) or the glm and Kruskal Wallis tests (aldex.glm). Reports both P and fdr values calculated by the Benjamini Hochberg correction.

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>ALDEx2</artifactId>
    <version>1.8.0-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:ALDEx2')

Test Results

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

Source

R

Release History