CRAN

MultiSV 0.0-67

MultiSV: an R package for identification of structural variations in multiple populations based on whole genome resequencing

Released Aug 27, 2014 by Khurram Maqbool

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

Dependencies

reshape 0.8.7 nlme 3.1-137

MultiSV is an R package for identification of structural variations in multiple populations based on whole genome resequencing. It fits linear mixed model and identifies structural variations in multiple populations using whole genome sequencing data. It could also be manipulated to use on RNA-seq data for differential gene expression (implementation in future releases). Main steps for analysis include generating read depth in bins using ComputeBinCounts. conversion of bins to MultiSV format using Bin2MultiSV. Finally, identification of structural variations using CallMultiSV.

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.cran</groupId>
    <artifactId>MultiSV</artifactId>
    <version>0.0-67-b37</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.cran:MultiSV')

Test Results

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

GetTestCfgFile-examples

Source

View GitHub Mirror