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simona

Semantic Similarity in Bio-Ontologies


Bioconductor version: Release (3.18)

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]

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

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

Installation

To install this package, start R (version "4.3") 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")
01. ontology_DAG: a class for ontology data HTML R Script
02. Gene Ontology HTML R Script
03. Import ontology files HTML R Script
04. Information content HTML R Script
05. Term similarity HTML R Script
06. Similarity between two groups of terms HTML R Script
07. Visualize DAGs HTML R Script
08. Random DAGs HTML R Script
09. Shiny app HTML R Script
10. Functional enrichment HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Annotation, BiomedicalInformatics, GO, Software
Version 1.0.10
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
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
System Requirements Perl, Java
URL https://github.com/jokergoo/simona
Bug Reports https://github.com/jokergoo/simona/issues
See More
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
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_1.0.10.tar.gz
Windows Binary simona_1.0.10.zip
macOS Binary (x86_64) simona_1.0.10.tgz
macOS Binary (arm64) simona_1.0.10.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
Old Source Packages for BioC 3.18 Source Archive