RRVGO

Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.

Introduction to rrvgo

Gene Ontologies (GO) are often used to guide the interpretation of high-throughput omics experiments, with lists of differentially regulated genes being summarized into sets of genes with a common functional representation. Due to the hierachical nature of Gene Ontologies, the resulting lists of enriched sets are usually redundant and difficult to interpret.

rrvgo aims at simplifying the redundance of GO sets by grouping similar terms in terms of semantic similarity. It also provides some plots to help with interpreting the summarized terms.

This software is heavily influenced by REVIGO. It mimics a good part of its core functionality, and even some of the outputs are similar. Without aims to compete, rrvgo tries to offer a programatic interface using available annotation databases and semantic similarity methods implemented in the Bioconductor project.

Installation

To install this package, start R and enter:

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

BiocManager::install("rrvgo")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

or access the pkgdown documentation.

Dependencies

Imports (mandatory for core functionality)

  • GOSemSim: Semantic similarity computation among GO terms.
  • AnnotationDbi: Provides user interface and database connection code for annotation data packages using SQLite data storage.
  • GO.db: Annotation maps describing the entire Gene Ontology assembled using data from GO.

Suggests

Citation

Sayols, S (2023). rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. microPublication Biology. doi: 10.17912/micropub.biology.000811.