simona

DOI: 10.18129/B9.bioc.simona  

Semantic Similarity in Bio-Ontologies

Bioconductor version: Release (3.18)

The package implements a rich set of methods for semantic similarity analysis on bio-ontologies. They include methods for information contents, similarities between two terms as well as similarities between two groups of terms. It also implements visualizations on DAGs.

Author: Zuguang Gu [aut, cre]

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

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")

 

HTML	R Script	1. ontology_DAG: a class for ontology data
HTML	R Script	2. Gene Ontology
HTML	R Script	3. Import ontology files
HTML	R Script	4. Information content
HTML	R Script	5. Term similarity
HTML	R Script	6. Similarity between two groups of terms
HTML	R Script	7. Visualize DAGs
HTML	R Script	8. Random DAGs
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Annotation, BiomedicalInformatics, GO, Software
Version	1.0.1
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
LinkingTo	Rcpp
Suggests	knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png
SystemRequirements	Perl, Java
Enhances
URL	https://github.com/jokergoo/simona
BugReports	https://github.com/jokergoo/simona/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	simona_1.0.1.tar.gz
Windows Binary	simona_1.0.1.zip (64-bit only)
macOS Binary (x86_64)	simona_1.0.1.tgz
macOS Binary (arm64)	simona_1.0.0.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
Old Source Packages for BioC 3.18	Source Archive