OGRE

DOI: 10.18129/B9.bioc.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>

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")

 

HTML	R Script	OGRE
PDF		Reference Manual
Text		NEWS

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
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_1.4.0.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
Old Source Packages for BioC 3.17	Source Archive