simona

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see simona.

Semantic Similarity in Bio-Ontologies

Bioconductor version: 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, BiomedicalInformatics, GO, Software

Version 1.0.10

In Bioconductor since BioC 3.18 (R-4.3) (0.5 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

System Requirements Perl, Java

URL https://github.com/jokergoo/simona

Bug Reports https://github.com/jokergoo/simona/issues

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