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:
GOaGO_1.1.1.tar.gz
GOaGO_1.1.1.zip(r-4.7)GOaGO_1.1.1.zip(r-4.6)GOaGO_1.1.1.zip(r-4.5)
GOaGO_1.1.1.tgz(r-4.6-any)GOaGO_1.1.1.tgz(r-4.5-any)
GOaGO_1.1.1.tar.gz(r-4.7-any)GOaGO_1.1.1.tar.gz(r-4.6-any)
GOaGO_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GOaGO/json (API)
NEWS
| # 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
- 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)
Last updated from:445fd480aa. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 271 | ||
| linux-devel-x86_64 | OK | 615 | ||
| source / vignettes | OK | 755 | ||
| linux-release-x86_64 | OK | 597 | ||
| macos-release-arm64 | OK | 382 | ||
| macos-oldrel-arm64 | OK | 360 | ||
| windows-devel | OK | 604 | ||
| windows-release | OK | 549 | ||
| windows-oldrel | OK | 592 | ||
| wasm-release | OK | 252 |
Exports:annotateAnchorsannotateInteractionsas.data.frameconvertTranscriptsToTSSDotPlotgenePairsGOaGOkeyTypeorganismRidgePlotshowtermGenePairs
Dependencies:aisdkAnnotationDbiapeaplotaskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbslibcachemcallrcliclusterclusterProfilercodetoolscpp11crayoncurldata.tableDBIdigestDOSEdplyrenrichitenrichplotevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverformatRfsfutile.loggerfutile.optionsgdtoolsgenericsGenomeInfoDbGenomicRangesggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggridgesggtangleggtreeglueGO.dbGOSemSimgridGraphicsgsongtablehighrhtmltoolshtmlwidgetshttrhttr2igraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixmemoisemimenlmeopensslpatchworkpillarpkgconfigplyrpngpolyclipprocessxpspurrrqvalueR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownRSQLiteS4VectorsS7sassscalesscatterpieSeqinfosnowstringistringrsyssystemfontstibbletidydrtidyrtidyselecttidytreetinytextreeiotweenrUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlyulab.utils
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 |
