OGRE-package: OGRE package to calculate, analyze and visiualize overlap...

In svenbioinf/OGRE: Calculate, visualize and analyse overlap between genomic regions

OGRE package to calculate, analyze and visiualize overlap between annotated genomic region datasets

Description

OGRE calculates overlap between user defined annotated genomic region datasets. Any regions can be supplied such as public annotations (genes), genetic variation (SNPs, mutations), regulatory elements (TFBS, promoters, CpG islands) and basically all types of NGS output from sequencing experiments. After overlap calculation, key numbers help analyse the extend of overlaps which can also be visualized at a genomic level.

Details

The main functions are:

OGREDataSetFromDir - build an OGRE dataset from a user defined directory with GRanges annotation files.

• loadAnnotations - Load dataset files containing genomic regions annotation information from hard drive

OGREDataSet - build an empty OGRE dataset to flexibly add datasets from other sources like AnnotationHub or custom GRanges objects.

• addDataSetFromHub - adds datasets from AnnotationHub

• addGRanges - adds user defined GenomicRanges datasets

fOverlaps - Finds all overlaps between query and subject datasets
sumPlot - calculates key numbers, tables and plots
gvizPlot - generates a genomic plot around query elements with overlapping subject hits.

For additional information, see the package vignette, by typing vignette("OGRE"). Software-related questions or issues can be posted to the Bioconductor Support Site:

https://support.bioconductor.org

or on github:

https://https://github.com/svenbioinf/OGRE

Author(s)

Sven Berres, Jörg Gromoll, Marius Wöste, Sarah Sandmann, Sandra Laurentino

svenbioinf/OGRE documentation built on Jan. 30, 2023, 10:55 p.m.