CRAN
GPseq 0.5
gpseq: Using the generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments
Released Jul 6, 2011 by Sudeep Srivastava
This package is available for Renjin and there are no known compatibility issues.
Some functions for modeling sequence read counts as a generalized poisson model and to use this model for detecting differentially expressed genes in different conditions and differentially spliced exons.
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>GPseq</artifactId>
<version>0.5-b243</version>
</dependency>
</dependencies>
<repositories>
<repository>
<id>bedatadriven</id>
<name>bedatadriven public repo</name>
<url>https://nexus.bedatadriven.com/content/groups/public/</url>
</repository>
</repositories>
Renjin CLI
If you're using Renjin from the command line, you load this library by invoking:
library('org.renjin.cran:GPseq')
Test Results
This package was last tested against Renjin 0.9.2644 on Jun 1, 2018.
- calc_chisq_statistic-examples
- estimate_differential_expression-examples
- estimate_differential_splicing-examples
- estimate_exon_gene_expression-examples
- generalized_poisson_likelihood-examples
- likelihood_ratio_generalized_poisson_exon_gene-examples
- likelihood_ratio_poisson_exon_gene-examples
- likelihood_ratio_tissue_generalized_poisson-examples
- likelihood_ratio_tissue_poisson-examples
- perform_permutation_de-examples
- perform_permutation_ds-examples