Package: rrvgo 1.25.0

Sergi Sayols

rrvgo: Reduce + Visualize GO

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

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

# Install 'rrvgo' in R:

install.packages('rrvgo', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:rrvgo-1.25.0(bioc 3.24)rrvgo-1.24.0(bioc 3.23)

Last updated from:4cffb83add. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	481
linux-devel-x86_64	NOTE	1034
source / vignettes	OK	608
linux-release-x86_64	NOTE	950
macos-release-arm64	NOTE	568
macos-oldrel-arm64	NOTE	576
windows-devel	NOTE	815
windows-release	NOTE	842
windows-oldrel	NOTE	823
wasm-release	OK	435

Last update: 2023-10-17
Started: 2020-02-27

Help page	Topics
calculateSimMatrix Calculate the score similarity matrix between terms	calculateSimMatrix
getGoSize Get GO term size (# of genes)	getGoSize
getGoTerm Get the description of a GO term	getGoTerm
getTermDisp Calculate the term dispensability score, defined as the semantic similarity threshold a term was assigned to a cluster (namely, the similarity of a term to the cluster representative term).	getTermDisp
getTermUniq Calculate the term uniqueness score, defined as 1 minus the average semantic similarity of a term to all other terms.	getTermUniq
gg_color_hue Emulate ggplot2 color palette.	gg_color_hue
heatmapPlot Plot similarity matrix as a heatmap	heatmapPlot
loadOrgdb Load an orgdb object	loadOrgdb
reduceSimMatrix Reduce a set of GO terms based on their semantic similarity and scores.	reduceSimMatrix
scatterPlot Plot GO terms as scattered points.	scatterPlot
shiny_rrvgo Launch an interactive web interface.	shiny_rrvgo
treemapPlot Plot GO terms as a treemap.	treemapPlot
wordlcoudPlot Plot GO reduced terms as a wordcloud.	wordcloudPlot