CRAN
MiClip 1.3
A Model-based Approach to Identify Binding Sites in CLIP-Seq Data
Released Nov 27, 2014 by Tao Wang
Dependencies
Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Here we present MiClip,a novel model-based approach to identify high-confidence protein-RNA binding sites in CLIP-Seq datasets. This approach assigns confidence value to each binding site on a probabilistic basis. The MiClip package can be flexibly applied to analyze both HITS-CLIP data and PAR-CLIP data.
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>MiClip</artifactId>
<version>1.3-b40</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:MiClip')
Test Results
This package was last tested against Renjin 0.9.2644 on Jun 2, 2018.