BioConductor

GenomicRanges 1.32.7

Representation and manipulation of genomic intervals and variables defined along a genome

Dependencies

XVector 0.20.0 IRanges 2.14.12 S4Vectors 0.18.3 GenomeInfoDb 1.16.0 BiocGenerics 0.26.0

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.

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.bioconductor</groupId>
    <artifactId>GenomicRanges</artifactId>
    <version>1.32.7-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.bioconductor:GenomicRanges')

Test Results

This package was last tested against Renjin 0.9.2692 on Oct 22, 2018.

• GNCList-class-examples
• GRanges-class-examples
• GRangesList-class-examples
• GenomicRanges-comparison-examples
• absoluteRanges-examples
• constraint-examples
• coverage-methods-examples
• findOverlaps-methods-examples
• genomic-range-squeezers-examples
• genomicvars-examples
• intra-range-methods-examples
• makeGRangesFromDataFrame-examples
• makeGRangesListFromDataFrame-examples
• nearest-methods-examples
• phicoef-examples
• run_unitTests
• setops-methods-examples
• strand-utils-examples
• tile-methods-examples
• tileGenome-examples

Source

Release History

• 1.32.7
• 1.32.6
• 1.32.4
• 1.32.3
• 1.32.2
• 1.32.1
• 1.32.0
• 1.31.23
• 1.31.22
• 1.31.21
• 1.31.20
• 1.31.19
• 1.31.18
• 1.31.17
• 1.31.16
• 1.31.15
• 1.31.14
• 1.31.13
• 1.31.12
• 1.31.11
• 1.31.9
• 1.31.8
• 1.31.6
• 1.31.3
• 1.28.6
• 1.24.3
• 1.22.4
• 1.20.8