simona

Semantic Similarity on Bio-Ontologies

Bioconductor version: 3.23 · Package version: 1.10.0

This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.

Installation

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

BiocManager::install("simona")

Details

Maintainer	Zuguang Gu <guzuguang@suat-sz.edu.cn>
Author	Zuguang Gu [aut, cre] (ORCID: <https://orcid.org/0000-0002-7395-8709>)
License	MIT + file LICENSE
URL	https://github.com/jokergoo/simona
Bug Reports	https://github.com/jokergoo/simona/issues
System Requirements	Perl, Java
Downloads rank	1029
Source branch	RELEASE_3_23
biocViews	Annotation, BiomedicalInformatics, GO, Software

Documentation

The simona package

Download

Source package

Dependencies

Depends: R (>= 4.1.0)

Imports: methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions, igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize, ComplexHeatmap, grDevices, stats, utils, shiny, fastmatch

LinkingTo: Rcpp

Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite

Reverse dependencies

Imports Me (2): GeDi, simplifyEnrichment