simona

This is the released version of simona; for the devel version, see simona.

Semantic Similarity on Bio-Ontologies

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.simona

Bioconductor version: Release (3.22)

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.

Author: Zuguang Gu [aut, cre] ORCID iD ORCID: 0000-0002-7395-8709

Maintainer: Zuguang Gu <z.gu at dkfz.de>

Citation (from within R, enter citation("simona")):

Installation

To install this package, start R (version "4.5") and enter:


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

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("simona")

The simona package HTML

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, BiomedicalInformatics, GO, Software

Version 1.8.0

In Bioconductor since BioC 3.18 (R-4.3) (2 years)

License MIT + file LICENSE

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

System Requirements Perl, Java

URL https://github.com/jokergoo/simona

Bug Reports https://github.com/jokergoo/simona/issues

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

Linking To Rcpp

Enhances

Depends On Me

Imports Me simplifyEnrichment

Suggests Me

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package simona_1.8.0.tar.gz

Windows Binary (x86_64) simona_1.7.1.zip

macOS Binary (x86_64) simona_1.8.0.tgz

macOS Binary (arm64) simona_1.8.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/simona

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/simona

Bioc Package Browser https://code.bioconductor.org/browse/simona/

Package Short Url https://bioconductor.org/packages/simona/

Package Downloads Report Download Stats