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Bioconductor - simona (development version)

simona

This is the development version of simona; for the stable release version, see simona.

Semantic Similarity on Bio-Ontologies

Bioconductor version: Development (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: 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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews Annotation, BiomedicalInformatics, GO, Software Version 1.7.1 In Bioconductor since BioC 3.18 (R-4.3) (1.5 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 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 simplifyEnrichment Suggests Me Links To Me Build Report Build Report Package Archives

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

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