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>

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")

 

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

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