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OGRE

Calculate, visualize and analyse overlap between genomic regions

Bioconductor version: 3.23 · Package version: 1.16.0

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.

Installation

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

BiocManager::install("OGRE")

Details

MaintainerSven Berres <svenbioinf@gmail.com>
AuthorSven Berres [aut, cre], Jörg Gromoll [ctb], Marius Wöste [ctb], Sarah Sandmann [ctb], Sandra Laurentino [ctb]
LicenseArtistic-2.0
URLhttps://github.com/svenbioinf/OGRE/
Bug Reportshttps://github.com/svenbioinf/OGRE/issues
Downloads rank411
Source branchRELEASE_3_23
biocViewsAnnotation, BiologicalQuestion, Metagenomics, Sequencing, Software, Visualization, WorkflowStep

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packageOGRE_1.16.0.tar.gz
Windows binary (x86_64)OGRE_1.16.0.zip
macOS binary (arm64)OGRE_1.16.0.tgz
macOS binary (x86_64)OGRE_1.16.0.tgz
Dependencies

Depends: R (>= 4.2.0), S4Vectors

Imports: GenomicRanges, methods, data.table, assertthat, ggplot2, Gviz, IRanges, AnnotationHub, grDevices, stats, Seqinfo, GenomeInfoDb, shiny, shinyFiles, DT, rtracklayer, shinydashboard, shinyBS, tidyr

Suggests: testthat (>= 3.0.0), knitr (>= 1.36), rmarkdown (>= 2.11)