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Bioconductor version: Release (3.18)
The package implements a rich set of methods for semantic similarity analysis on bio-ontologies. They include methods for information contents, similarities between two terms as well as similarities between two groups of terms. It also implements visualizations on DAGs.
Maintainer: Zuguang Gu <z.gu at dkfz.de>
Citation (from within R,
enter citation("simona")
):
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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("simona")
HTML | R Script | 1. ontology_DAG: a class for ontology data |
HTML | R Script | 2. Gene Ontology |
HTML | R Script | 3. Import ontology files |
HTML | R Script | 4. Information content |
HTML | R Script | 5. Term similarity |
HTML | R Script | 6. Similarity between two groups of terms |
HTML | R Script | 7. Visualize DAGs |
HTML | R Script | 8. Random DAGs |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | Annotation, BiomedicalInformatics, GO, Software |
Version | 1.0.1 |
In Bioconductor since | BioC 3.18 (R-4.3) (< 6 months) |
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 |
LinkingTo | Rcpp |
Suggests | knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png |
SystemRequirements | Perl, Java |
Enhances | |
URL | https://github.com/jokergoo/simona |
BugReports | https://github.com/jokergoo/simona/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | simona_1.0.1.tar.gz |
Windows Binary | simona_1.0.1.zip (64-bit only) |
macOS Binary (x86_64) | simona_1.0.1.tgz |
macOS Binary (arm64) | simona_1.0.0.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 |
Old Source Packages for BioC 3.18 | Source Archive |
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