OGRE
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see OGRE.
Calculate, visualize and analyse overlap between genomic regions
Bioconductor version: 3.15
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("OGRE")):
Installation
To install this package, start R (version "4.2") 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 | ||
| NEWS | Text |
Details
| biocViews | Annotation, BiologicalQuestion, Metagenomics, Sequencing, Software, Visualization, WorkflowStep |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2 years) |
| 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 |
| System Requirements | |
| URL | https://github.com/svenbioinf/OGRE/ |
| Bug Reports | https://github.com/svenbioinf/OGRE/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr (>= 1.36), rmarkdown (>= 2.11) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | OGRE_1.0.0.tar.gz |
| Windows Binary | OGRE_1.0.0.zip |
| macOS Binary (x86_64) | OGRE_1.0.0.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 3.15 | Source Archive |