GOSemSim
GO-terms Semantic Similarity Measures
Bioconductor version: 3.23 · Package version: 2.38.3
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GOSemSim")Details
| Maintainer | Guangchuang Yu <guangchuangyu@gmail.com> |
| Author | Guangchuang Yu [aut, cre], Alexey Stukalov [ctb], Pingfan Guo [ctb], Chuanle Xiao [ctb], Lluís Revilla Sancho [ctb] |
| License | Artistic-2.0 |
| URL | https://yulab-smu.top/biomedical-knowledge-mining-book/ |
| Bug Reports | https://github.com/YuLab-SMU/GOSemSim/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, Clustering, GO, Network, Pathways, Software |
| Package Short Url | https://bioconductor.org/packages/GOSemSim/ |
Citation
From within R, enter citation("GOSemSim"):
Guangchuang Yu. GOSemSim: GO-terms Semantic Similarity Measures. doi:10.18129/B9.bioc.GOSemSim, R package version 2.38.3, https://bioconductor.org/packages/GOSemSim.
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 | GOSemSim_2.38.3.tar.gz |
| Windows binary (x86_64) | GOSemSim_2.38.3.zip |
| macOS binary (arm64) | GOSemSim_2.38.3.tgz |
| macOS binary (x86_64) | GOSemSim_2.38.3.tgz |
Dependencies
Depends: R (>= 4.2.0)
Imports: AnnotationDbi, DBI, digest, GO.db, methods, rlang, stats, utils, yulab.utils (>= 0.2.3)
LinkingTo: Rcpp
Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR
Reverse dependencies
Depends On Me (1): tRanslatome
Imports Me (7): clusterProfiler, DOSE, enrichplot, meshes, Rcpi, rrvgo, ViSEAGO
Suggests Me (7): BioCor, epiNEM, FELLA, genekitr, protr, scDiffCom, SemDist