simona
Semantic Similarity on Bio-Ontologies
Bioconductor version: 3.23 · Package version: 1.10.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("simona")Details
| Maintainer | Zuguang Gu <guzuguang@suat-sz.edu.cn> |
| Author | Zuguang Gu [aut, cre] (ORCID: <https://orcid.org/0000-0002-7395-8709>) |
| License | MIT + file LICENSE |
| URL | https://github.com/jokergoo/simona |
| Bug Reports | https://github.com/jokergoo/simona/issues |
| System Requirements | Perl, Java |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, BiomedicalInformatics, GO, Software |
| Package Short Url | https://bioconductor.org/packages/simona/ |
Citation
From within R, enter citation("simona"):
Zuguang Gu. simona: Semantic Similarity on Bio-Ontologies. doi:10.18129/B9.bioc.simona, R package version 1.10.0, https://bioconductor.org/packages/simona.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | simona_1.10.0.tar.gz |
| Windows binary (x86_64) | simona_1.10.0.zip |
| macOS binary (arm64) | simona_1.10.0.tgz |
| macOS binary (x86_64) | simona_1.10.0.tgz |
Dependencies
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
LinkingTo: Rcpp
Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite
Reverse dependencies
Imports Me (2): GeDi, simplifyEnrichment