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 < at>

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


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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


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,, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png
SystemRequirements Perl, Java
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package simona_1.0.1.tar.gz
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macOS Binary (x86_64) simona_1.0.1.tgz
macOS Binary (arm64) simona_1.0.0.tgz
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