Package: goSorensen 1.7.0
Pablo Flores
goSorensen: Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)
This package implements inferential methods to compare gene lists in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items.
Authors:
goSorensen_1.7.0.tar.gz
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goSorensen_1.7.0.tgz(r-4.4-any)goSorensen_1.7.0.tgz(r-4.3-any)
goSorensen_1.7.0.tar.gz(r-4.5-noble)goSorensen_1.7.0.tar.gz(r-4.4-noble)
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goSorensen.pdf |goSorensen.html✨
goSorensen/json (API)
NEWS
# Install 'goSorensen' in R: |
install.packages('goSorensen', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- BP.4 - An example of an object of class "equivSDhtestList" resulting from a call to 'equivSorensenTest'
- allOncoGeneLists - 7 gene lists possibly related with cancer
- allTabs - An example of an object of class "allTableList" resulting from a call to 'buildEnrichTable'
- allTabsBP.4 - An example of an object of class "tableList" resulting from a call to 'buildEnrichTable'
- boot.cancerEquivSorensen - An example of object of class "AllEquivSDhtest" resulting from a call to 'allEquivTestSorensen'
- cancerEquivSorensen - An example of an object of class "AllEquivSDhtest" resulting from a call to 'allEquivTestSorensen'
- humanEntrezIDs - Entrez Identifiers for all human genes contained in the org.Hs.eg.db package.
- pbtGeneLists - 5 gene lists possibly related with kidney transplant rejection
- tab_atlas.sanger_BP3 - Cross-tabulation of enriched GO items at level 3 of ontology BP in two gene lists
- waldman_atlas.BP.4 - An example of an object of class "equivSDhtest" resulting from a call to function 'equivSorensenTest'
On BioConductor:goSorensen-1.7.0(bioc 3.20)goSorensen-1.6.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:2be7d70d18
Exports:allBuildEnrichTableallEquivTestSorensenallHclustThresholdallSorenThresholdbuildEnrichTabledSorensenduppSorensenequivTestSorensengetDissimilaritygetEffNbootgetNbootgetPvaluegetSEgetTablegetUpperhclustThresholdnice2x2TablepruneClustsseSorensensorenThresholdupgrade
Dependencies:AnnotationDbiapeaplotaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemcliclusterProfilercodetoolscolorspaceCompQuadFormcowplotcpp11crayoncurldata.tableDBIdigestDOSEdownloaderdplyrenrichplotfansifarverfastmapfastmatchfgseaformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggtreeglueGO.dbgoProfilesGOSemSimgraphlayoutsgridExtragridGraphicsgsongtableHDO.dbhttrigraphIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dbpatchworkpillarpkgconfigplogrplyrpngpolyclippurrrqvalueR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangRSQLiteS4VectorsscalesscatterpieshadowtextsnowstringistringrsyssystemfontstibbletidygraphtidyrtidyselecttidytreetreeiotweenrUCSC.utilsutf8vctrsviridisviridisLitewithrXVectoryulab.utilszlibbioc