BioConductor

ALDEx2 1.12.0

Analysis Of Differential Abundance Taking Sample Variation Into Account

Released Oct 11, 2017 by Greg Gloor

This package can be loaded by Renjin but 3 out 21 tests failed. An older version of this package is more compatible with Renjin.

Dependencies

GenomicRanges 1.32.6 IRanges 2.14.10 BiocParallel 1.14.2 S4Vectors 0.18.3 SummarizedExperiment 1.10.1 multtest 2.36.0

A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcox rank test or Welch t-test (via aldex.ttest), or a glm and Kruskal-Wallis test (via aldex.glm). Reports p-values and Benjamini-Hochberg corrected p-values.

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>1.12.0-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:ALDEx2')

Test Results

This package was last tested against Renjin 0.9.2689 on Aug 26, 2018.