CRAN

ioncopy 2.1.1

Calling Copy Number Alterations in Amplicon Sequencing Data

Released Mar 23, 2018 by Jan Budczies

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

Dependencies

Method for the calculation of copy numbers and calling of copy number alterations. The algorithm uses coverage data from amplicon sequencing of a sample cohort as input. The method includes significance assessment, correction for multiple testing and does not depend on normal DNA controls. Budczies (2016 Mar 15) .

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>ioncopy</artifactId>
    <version>2.1.1-b1</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:ioncopy')

Test Results

This package was last tested against Renjin 0.9.2615 on Mar 27, 2018.

coverage-examples

Source

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