Package: GeDi 1.1.1
Annekathrin Nedwed
GeDi: Defining and visualizing the distances between different genesets
The package provides different distances measurements to calculate the difference between genesets. Based on these scores the genesets are clustered and visualized as graph. This is all presented in an interactive Shiny application for easy usage.
Authors:
GeDi_1.1.1.tar.gz
GeDi_1.1.1.zip(r-4.5)GeDi_1.1.1.zip(r-4.4)GeDi_1.1.1.zip(r-4.3)
GeDi_1.1.1.tgz(r-4.4-any)GeDi_1.1.1.tgz(r-4.3-any)
GeDi_1.1.1.tar.gz(r-4.5-noble)GeDi_1.1.1.tar.gz(r-4.4-noble)
GeDi_1.1.1.tgz(r-4.4-emscripten)GeDi_1.1.1.tgz(r-4.3-emscripten)
GeDi.pdf |GeDi.html✨
GeDi/json (API)
NEWS
# Install 'GeDi' in R: |
install.packages('GeDi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/annekathrinsilvia/gedi/issues
- macrophage_KEGG_example - A sample input RData file
- macrophage_Reactome_example - A sample input RData file
- macrophage_topGO_example - A sample input RData file
- macrophage_topGO_example_small - A small sample input RData file
- ppi_macrophage_topGO_example_small - PPI
- sample_geneset - A sample input text file
- sample_geneset_broken - A broken input text file
- sample_geneset_empty - An empty input text file
- sample_geneset_small - A small sample input text file
- scores_macrophage_topGO_example_small - Sample scores
On BioConductor:GeDi-1.1.0(bioc 3.20)GeDi-1.0.0(bioc 3.19)
Last updated 15 days agofrom:a17c59cdff
Exports:buildClusterGraphbuildGraphbuildHistogramDatacalculateJaccardcalculateKappacalculateSorensenDicecheckInclusionclusteringdistanceDendrodistanceHeatmapenrichmentWordcloudfuzzyClusteringGeDigetAdjacencyMatrixgetAnnotationgetBipartiteGraphgetClusterAdjacencyMatrixgetGenesgetGraphTitlegetIdgetInteractionScoregetJaccardMatrixgetKappaMatrixgetMeetMinMatrixgetpMMMatrixgetPPIgetSorensenDiceMatrixgetStringDBgoSimilaritygsHistogramkNN_clusteringpMMlocalscaleGOseedFinding
Dependencies:abindAnnotationDbianytimeaskpassbackbonebase64encBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelBiostringsbitbit64bitopsblobbs4DashbslibcachemcaToolscellrangerchroncirclizecliclueclustercodetoolscolorspacecolourpickercommonmarkComplexHeatmapComplexUpsetcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydendextendDESeq2digestdoParalleldplyrDTdynamicTreeCutevaluateexpmfansifarverfastmapfilelockfontawesomeforeachformatRfreshfsfutile.loggerfutile.optionsgenericsGeneTonicGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggdendroggforceggplot2ggrepelggridgesGlobalOptionsglueGO.dbGOSemSimgplotsgridExtragsubfngtablegtoolshashhighrhmshtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeNLPopensslpatchworkpillarpkgconfigplogrplotlyplotrixplyrpngpolyclipprettyunitsprogresspromisesprotopurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppHNSWreadxlrematchrintrojsrjsonrlangrmarkdownRSQLiterstudioapiS4ArraysS4VectorssassscalesshapeshinyshinyAceshinyBSshinycssloadersshinyjsshinyWidgetsslamsnowsourcetoolsSparseArraysqldfSTRINGdbstringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttinytextippytmtweenrUCSC.utilsutf8vctrsviridisviridisLitevisNetworkwaiterwithrwordcloud2xfunxml2xtableXVectoryamlyulab.utilszlibbioc