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OGRE

Calculate, visualize and analyse overlap between genomic regions

Bioconductor version: Release (3.17)

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 "4.3") and enter: 

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

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")
OGRE HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, BiologicalQuestion, Metagenomics, Sequencing, Software, Visualization, WorkflowStep
Version 1.4.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2.0), S4Vectors
Imports GenomicRanges, methods, data.table, assertthat, ggplot2, Gviz, IRanges, AnnotationHub, grDevices, stats, GenomeInfoDb, shiny, shinyFiles, DT, rtracklayer, shinydashboard, shinyBS, tidyr
Linking To
Suggests testthat (>= 3.0.0), knitr (>= 1.36), rmarkdown (>= 2.11)
System Requirements
Enhances
URL https://github.com/svenbioinf/OGRE/
Bug Reports https://github.com/svenbioinf/OGRE/issues
See More
Depends On Me
Imports Me
Suggests Me
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Build Report  

Package Archives

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

Source Package OGRE_1.4.0.tar.gz
Windows Binary OGRE_1.4.0.zip
macOS Binary (x86_64) OGRE_1.4.0.tgz
macOS Binary (arm64) OGRE_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/OGRE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/OGRE
Bioc Package Browser https://code.bioconductor.org/browse/OGRE/
Package Short Url https://bioconductor.org/packages/OGRE/
Package Downloads Report Download Stats