CRAN

rphast 1.6.9

Interface to 'PHAST' Software for Comparative Genomics

Released Feb 11, 2018 by Ritika Ramani

This package can be loaded by Renjin but there was an error compiling C/FORTRAN sources and 78 out 88 tests failed.

Provides an R interface to the 'PHAST'() software (Phylogenetic Analysis with Space/Time Models). It can be used for many types of analysis in comparative and evolutionary genomics, such as estimating models of evolution from sequence data, scoring alignments for conservation or acceleration, and predicting elements based on conservation or custom phylogenetic hidden Markov models. It can also perform many basic operations on multiple sequence alignments and phylogenetic trees.

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>rphast</artifactId>
    <version>1.6.9-b5</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:rphast')

Test Results

This package was last tested against Renjin 0.9.2644 on Jun 1, 2018.

Source

R
C

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Release History