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Bioconductor - GOSemSim

GOSemSim

This is the released version of GOSemSim; for the devel version, see GOSemSim.

GO-terms Semantic Similarity Measures

Bioconductor version: Release (3.21)

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 (from within R, enter citation("GOSemSim")): Installation

To install this package, start R (version "4.5") 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")
Details biocViews Annotation, Clustering, GO, Network, Pathways, Software Version 2.34.0 In Bioconductor since BioC 2.4 (R-2.9) (16 years) License Artistic-2.0 Depends R (>= 4.2.0) Imports AnnotationDbi, DBI, digest, GO.db, methods, rlang, R.utils, stats, utils, yulab.utils (>= 0.1.6) 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 clusterProfiler, DOSE, enrichplot, GeDi, meshes, Rcpi, rrvgo, scQTLtools, ViSEAGO, BiSEp Suggests Me BioCor, epiNEM, FELLA, SemDist, genekitr, protr, scDiffCom Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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