GOSemSim
GO-terms Semantic Similarity Measures
Bioconductor version: Release (3.19)
The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.
Author: Guangchuang Yu [aut, cre], Alexey Stukalov [ctb], Pingfan Guo [ctb], Chuanle Xiao [ctb], Lluís Revilla Sancho [ctb]
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
citation("GOSemSim")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GOSemSim")
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("GOSemSim")| GOSemSim | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Clustering, GO, Network, Pathways, Software |
| Version | 2.30.2 |
| In Bioconductor since | BioC 2.4 (R-2.9) (15.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0) |
| Imports | AnnotationDbi, DBI, digest, GO.db, httr2, methods, rlang, R.utils, stats, utils, yulab.utils |
| System Requirements | |
| URL | https://yulab-smu.top/biomedical-knowledge-mining-book/ |
| Bug Reports | https://github.com/YuLab-SMU/GOSemSim/issues |
See More
| Suggests | AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, rappdirs, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | tRanslatome |
| Imports Me | DOSE, GeDi, Rcpi, ViSEAGO, clusterProfiler, enrichplot, meshes, rrvgo, simplifyEnrichment, BiSEp |
| Suggests Me | BioCor, FELLA, SemDist, epiNEM, genekitr, protr, scDiffCom |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GOSemSim_2.30.2.tar.gz |
| Windows Binary (x86_64) | GOSemSim_2.30.2.zip |
| macOS Binary (x86_64) | GOSemSim_2.30.2.tgz |
| macOS Binary (arm64) | GOSemSim_2.30.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GOSemSim |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GOSemSim |
| Bioc Package Browser | https://code.bioconductor.org/browse/GOSemSim/ |
| Package Short Url | https://bioconductor.org/packages/GOSemSim/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |