GOSemSim
This is the development version of GOSemSim; for the stable release version, see GOSemSim.
GO-terms Semantic Similarity Measures
Bioconductor version: Development (3.24)
Semantic similarity analysis of Gene Ontology (GO) annotations provides a quantitative framework for comparing GO terms, gene products, and gene clusters. GOSemSim implements widely used information content- and graph-based similarity measures, including the methods of Resnik, Schlicker, Jiang, Lin, Wang and TCSS. It also provides utilities for preparing annotation data and combining term-level similarities into gene- and cluster-level scores.
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 "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Clustering, GO, Network, Pathways, Software |
| Version | 2.39.2 |
| In Bioconductor since | BioC 2.4 (R-2.9) (17 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2.0) |
| Imports | AnnotationDbi, DBI, digest, GO.db, methods, rlang, stats, utils, yulab.utils (>= 0.2.3) |
| System Requirements | |
| URL | https://yulab-smu.top/biomedical-knowledge-mining-book/ |
| Bug Reports | https://github.com/YuLab-SMU/GOSemSim/issues |
See More
| Suggests | AnnotationHub, BiocParallel, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, quarto, readr, testthat, tidyr, tidyselect, ROCR |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | tRanslatome |
| Imports Me | clusterProfiler, DOSE, enrichplot, meshes, Rcpi, rrvgo, ViSEAGO |
| 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.
| Source Package | GOSemSim_2.39.2.tar.gz |
| Windows Binary (x86_64) | GOSemSim_2.39.2.zip |
| macOS Binary (big-sur-x86_64) | GOSemSim_2.39.2.tgz |
| macOS Binary (sonoma-arm64) | GOSemSim_2.39.2.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 |