simona
Semantic Similarity in Bio-Ontologies
Bioconductor version: Release (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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
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 | |
| 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 |