CRAN

AmpliconDuo 1.1

Statistical Analysis of Amplicon Data of the Same Sample to Identify Artefacts

Released Jan 19, 2016 by Anja Lange [aut, cre], Daniel Hoffmann [aut]

This package can be loaded by Renjin but 6 out 11 tests failed.

Dependencies

ggplot2 2.0.0 xtable 1.8-0

Increasingly powerful techniques for high-throughput sequencing open the possibility to comprehensively characterize microbial communities, including rare species. However, a still unresolved issue are the substantial error rates in the experimental process generating these sequences. To overcome these limitations we propose an approach, where each sample is split and the same amplification and sequencing protocol is applied to both halves. This procedure should allow to detect likely PCR and sequencing artifacts, and true rare species by comparison of the results of both parts. The AmpliconDuo package, whereas amplicon duo from here on refers to the two amplicon data sets of a split sample, is intended to help interpret the obtained read frequency distribution across split samples, and to filter the false positive reads.

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>AmpliconDuo</artifactId>
    <version>1.1-b18</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:AmpliconDuo')

Test Results

This package was last tested against Renjin 0.8.2359 on May 26, 2017.

Source

R

View GitHub Mirror

Release History