Package: GOaGO 1.1.1

Aleksander Jankowski

GOaGO: Gene Ontology enrichment analysis of gene pairs

GO-a-GO annotates Gene Ontology terms that are enriched in a given set of gene pairs. The enrichment is calculated from a permutation test for overrepresentation of gene pairs that are associated with a shared term. Such gene pairs are counted for the original set of gene pairs and compared against randomized sets in which the structure of the pairs is preserved, but the gene identities (including the associated terms) are permuted.

Authors:Aleksander Jankowski [aut, cre]

GOaGO_1.1.1.tar.gz
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GOaGO_1.1.1.tgz(r-4.6-any)GOaGO_1.1.1.tgz(r-4.5-any)
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GOaGO_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GOaGO/json (API)

# Install 'GOaGO' in R:

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

Bug tracker:https://github.com/ajank/goago/issues

Datasets:

genePairsGM12878 - Gene pairs associated with chromatin loops in GM12878 cell line

On BioConductor:GOaGO-1.1.1(bioc 3.24)GOaGO-1.0.1(bioc 3.23)

go genesetenrichment

4.70 score 1 stars 5 scripts 12 exports 134 dependencies

Last updated from:445fd480aa. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	293
linux-devel-x86_64	OK	592
source / vignettes	OK	710
linux-release-x86_64	OK	628
macos-release-arm64	OK	436
macos-oldrel-arm64	OK	338
windows-devel	OK	555
windows-release	OK	484
windows-oldrel	OK	567
wasm-release	OK	282

Exports:annotateAnchors annotateInteractions as.data.frame convertTranscriptsToTSS DotPlot genePairs GOaGO keyType organism RidgePlot show termGenePairs

Dependencies:aisdk AnnotationDbi ape aplot askpass base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob bslib cachem callr cli cluster clusterProfiler codetools cpp11 crayon curl data.table DBI digest DOSE dplyr enrichit enrichplot evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver formatR fs futile.logger futile.options gdtools generics GenomeInfoDb GenomicRanges ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggridges ggtangle ggtree glue GO.db GOSemSim gridGraphics gson gtable highr htmltools htmlwidgets httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix memoise mime nlme openssl otel patchwork pillar pkgconfig plyr png polyclip processx ps purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppEigen reshape2 rlang rmarkdown RSQLite S4Vectors S7 sass scales scatterpie Seqinfo snow stringi stringr sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex treeio tweenr UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml yulab.utils

Gene Ontology enrichment analysis of gene pairs with GO-a-GO

Rendered fromGOaGO.Rmdusingknitr::rmarkdown

Last update: 2026-04-22
Started: 2026-02-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Associate interaction anchors to the nearest TSSes	annotateAnchors
Associate interactions to gene pairs	annotateInteractions
Coerce a 'GOaGO-result' object to a data frame	as.data.frame as.data.frame,GOaGO-result-method
Convert gene transcripts to Transcription Start Sites	convertTranscriptsToTSS
Dotplot of the enriched Gene Ontology terms	DotPlot
Gene pairs associated with chromatin loops in GM12878 cell line	genePairsGM12878
Gene Ontology enrichment analysis in a set of gene pairs	GOaGO
Accessors and show method for 'GOaGO-result' objects	genePairs GOaGO-accessors keyType organism organism,GOaGO-result-method show show,GOaGO-result-method
An S4 class to represent the results of GO-a-GO enrichment analysis	GOaGO-result-class
Ridgeplot of the sampling distributions for the randomized gene pairs	RidgePlot
Extract the enriched Gene Ontology terms along with gene pairs sharing them	termGenePairs
Extract unique gene pairs from the data frame provided	uniqueGenePairs