simona
This is the development version of simona; for the stable release version, see simona.
Semantic Similarity on Bio-Ontologies
Bioconductor version: Development (3.21)
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:
Maintainer: Zuguang Gu <z.gu at dkfz.de>
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")| The simona package | HTML |
| Reference Manual | |
| NEWS | Text |
| LICENSE | Text |
Details
| biocViews | Annotation, BiomedicalInformatics, GO, Software |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| 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 |
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.
| Source Package | simona_1.5.0.tar.gz |
| Windows Binary (x86_64) | simona_1.5.0.zip (64-bit only) |
| macOS Binary (x86_64) | simona_1.5.0.tgz |
| macOS Binary (arm64) | simona_1.5.0.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 |