In altintasali/ontoClust: Cluster Gene Ontology Terms

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

ontoClust

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)

altintasali/ontoClust documentation built on Dec. 19, 2021, 1:36 a.m.