OGRE

DOI: 10.18129/B9.bioc.OGRE    

This is the development version of OGRE; for the stable release version, see OGRE.

Calculate, visualize and analyse overlap between genomic regions

Bioconductor version: Development (3.16)

OGRE calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs, or reads from sequencing experiments. Key numbers help analyse the extend of overlaps which can also be visualized at a genomic level.

Author: Sven Berres [aut, cre], Jörg Gromoll [ctb], Marius Wöste [ctb], Sarah Sandmann [ctb], Sandra Laurentino [ctb]

Maintainer: Sven Berres <svenbioinf at gmail.com>

Citation (from within R, enter citation("OGRE")):

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("OGRE")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("OGRE")

 

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PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, BiologicalQuestion, Metagenomics, Sequencing, Software, Visualization, WorkflowStep
Version 1.1.0
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
License Artistic-2.0
Depends R (>= 4.1.0), S4Vectors
Imports GenomicRanges, methods, data.table, assertthat, ggplot2, Gviz, IRanges, AnnotationHub, grDevices, stats, GenomeInfoDb, shiny, shinyFiles, DT, rtracklayer, shinydashboard, shinyBS, tidyr
LinkingTo
Suggests testthat (>= 3.0.0), knitr (>= 1.36), rmarkdown (>= 2.11)
SystemRequirements
Enhances
URL https://github.com/svenbioinf/OGRE/
BugReports https://github.com/svenbioinf/OGRE/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package OGRE_1.1.0.tar.gz
Windows Binary OGRE_1.1.0.zip
macOS 10.13 (High Sierra) OGRE_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/OGRE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/OGRE
Package Short Url https://bioconductor.org/packages/OGRE/
Package Downloads Report Download Stats

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