BioConductor

DEXSeq 1.26.0

Inference of differential exon usage in RNA-Seq

Released Apr 30, 2018 by Alejandro Reyes

This package can be loaded by Renjin but all tests failed.

Dependencies

statmod 1.4.30 DESeq2 1.20.0 geneplotter 1.58.0 RColorBrewer 1.1-2 stringr 1.3.1 S4Vectors 0.18.3 BiocParallel 1.14.2 SummarizedExperiment 1.10.1 Rsamtools 1.32.3 hwriter 1.3.2 AnnotationDbi 1.42.1 Biobase 2.40.0 genefilter 1.62.0 GenomicRanges 1.32.6 BiocGenerics 0.26.0 biomaRt 2.36.1 IRanges 2.14.10

The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

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>DEXSeq</artifactId>
    <version>1.26.0-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:DEXSeq')

Test Results

This package was last tested against Renjin 0.9.2689 on Aug 27, 2018.