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rrvgo

Reduce + Visualize GO


Bioconductor version: Release (3.18)

Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.

Author: Sergi Sayols [aut, cre], Sara Elmeligy [ctb]

Maintainer: Sergi Sayols <sergisayolspuig at gmail.com>

Citation (from within R, enter citation("rrvgo")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rrvgo")

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("rrvgo")
Using rrvgo HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Annotation, Clustering, GO, Network, Pathways, Software
Version 1.14.1
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-3
Depends
Imports GOSemSim, AnnotationDbi, GO.db, pheatmap, ggplot2, ggrepel, treemap, tm, wordcloud, shiny, grDevices, grid, stats, methods, umap
System Requirements
URL https://www.bioconductor.org/packages/rrvgo https://ssayols.github.io/rrvgo/index.html
See More
Suggests knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), shinydashboard, DT, plotly, heatmaply, magrittr, utils, clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me genekitr, scDiffCom
Links To Me
Build Report Build Report

Package Archives

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

Source Package rrvgo_1.14.1.tar.gz
Windows Binary rrvgo_1.14.1.zip
macOS Binary (x86_64) rrvgo_1.14.1.tgz
macOS Binary (arm64) rrvgo_1.14.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/rrvgo
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rrvgo
Bioc Package Browser https://code.bioconductor.org/browse/rrvgo/
Package Short Url https://bioconductor.org/packages/rrvgo/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive