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)
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)
For a quick start, I recommend checking the example code provided in the vignette:
library(ontoClust)
vignette(topic = "quickstart", package = "ontoClust")
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)