BioConductor

DRIMSeq 1.8.0

Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

Released May 24, 2017 by Malgorzata Nowicka

This package can be loaded by Renjin but 2 out 33 tests failed.

Dependencies

IRanges 2.14.10 limma 3.36.1 ggplot2 2.2.1 MASS 7.3-50 GenomicRanges 1.32.3 BiocParallel 1.14.1 edgeR 3.22.2 S4Vectors 0.18.2 reshape2 1.4.3 BiocGenerics 0.26.0

The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and 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>DRIMSeq</artifactId>
    <version>1.8.0-b2</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:DRIMSeq')

Test Results

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