/ontoClust

Cluster Gene Ontology Terms

Primary LanguageRGNU General Public License v3.0GPL-3.0

ontoClust

R-CMD-check

This packages clusters gene ontology terms. Currently supported gene ontology databases are

  • Gene Ontology (GO): Biological Process (BP)
  • Gene Ontology (GO): Molecular Function (MF)
  • Gene Ontology (GO): Cellular Component (CC)
  • Kyoto Encyclopedia of Genes and Genomes (KEGG): KEGG and KEGG Modules
  • REACTOME
  • Disease Ontology (DO)

Installation

Please install devtools if you haven’t yet.

install.packages("devtools")

Then, you basically install the ontoClust package by using:

library(devtools)
install_github("altintasali/ontoClust", build_vignettes = TRUE)

Quick Start

For a quick start, I recommend checking the example code provided in the vignette:

library(ontoClust)
vignette(topic = "quickstart", package = "ontoClust")

News and TO-DOs

This package is still under development.

News:

  • Network plot with facets
  • Support for other ontology terms (GO, KEGG, REACTOME, DO)
  • Support for human, mouse and rat

TO-DOs:

  • Same color scheme across plot functions
  • Support for KEGG Modules
  • Support for other species (yeast etc)
  • Plots will show view for multiple contrasts/groups
  • Analysis with using terms from multiple ontology database
  • Implement Word Clouds (with dendrograms)