BioConductor

annmap 1.18.0

Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

Released Sep 14, 2011 by Tim Yates

This package can be loaded by Renjin but 11 out 12 tests failed.

Dependencies

DBI 0.7 BiocGenerics 0.22.1 GenomicRanges 1.28.6 RMySQL digest 0.6.12 lattice 0.20-35 Biobase 2.36.2 IRanges 2.10.5 Rsamtools 1.28.0 genefilter 1.58.1

annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl.

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>annmap</artifactId>
    <version>1.18.0-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:annmap')

Test Results

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

Source

R

Release History