Package: categoryCompare 1.49.0
Robert M. Flight
categoryCompare: Meta-analysis of high-throughput experiments using feature annotations
Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).
Authors:
categoryCompare_1.49.0.tar.gz
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categoryCompare.pdf |categoryCompare.html✨
categoryCompare/json (API)
NEWS
| # Install 'categoryCompare' in R: |
| install.packages('categoryCompare', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rmflight/categorycompare/issues
- ccOpts - Test data for 'categoryCompare'
- ccResults - Test data for 'categoryCompare'
- ccResultsBPHier - Test data for 'categoryCompare'
- enrichLists - Test data for 'categoryCompare'
- gUniverse - Test data for 'categoryCompare'
- geneLists - Test data for 'categoryCompare'
- gseaRes - Test data for 'categoryCompare'
- table10 - Test data for 'categoryCompare'
- table48 - Test data for 'categoryCompare'
On BioConductor:categoryCompare-1.49.0(bioc 3.20)categoryCompare-1.48.0(bioc 3.19)
Last updated 2 months agofrom:0551947c25
Exports:allAnnotationannotationbreakEdgesccCompareccEnrichccOutCytccTypeccType<-compareColorscompareColors<-compareIndxcompareNamescompareNames<-cwReloadcytOutDatacytOutNodesfdrfdr<-fdrvaluesgeneAnnMappinggraphTypegraphType<-hyperGTestCClistNamesmainGraphmainTablemergeListsminCountminCount<-ontologyoutTypeoutType<-pvalueCutoffpvalueCutoff<-pvalueTypepvalueType<-resetColorssigID
Dependencies:annotateAnnotationDbiAnnotationForgeaskpassbackportsbase64encbase64urlBHBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemCategorycaToolsclicolorspacecpp11crayoncurlDBIdigestevaluatefansifastmapfsgenefilterGenomeInfoDbGenomeInfoDbDataglueGO.dbGOstatsgplotsgraphGSEABasegtoolshtmltoolshttrhwriterIRangesIRdisplayIRkerneljsonliteKEGGRESTKernSmoothlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpbdZMQpillarpkgconfigplogrpngR6RBGLRColorBrewerRCurlRCy3reprRgraphvizRJSONIOrlangRSQLiteS4VectorsstringisurvivalsysUCSC.utilsutf8uuidvctrsXMLxtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Meta-analysis of high-throughput experiments using feature annotations | categoryCompare-package categoryCompare |
| Methods for Function 'breakEdges' in Package 'categoryCompare' | breakEdges breakEdges,ccCompareResult,numeric-method breakEdges,numeric,numeric-method breakEdges-methods |
| Comparison of enriched annotations | ccCompare ccCompare,ccEnrichCollection,ccOptions-method ccCompare,GENccEnrichResult,ccOptions-method ccCompare,GOccEnrichResult,ccOptions-method ccCompare,KEGGccEnrichResult,ccOptions-method ccCompare-methods |
| Class '"ccCompareCollection"' | ccCompareCollection ccCompareCollection-class |
| Methods for Function 'ccCompareGeneric' in Package 'categoryCompare' | ccCompareGeneric ccCompareGeneric-methods ccOptions,ccCompareGeneric-method GENccEnrichResult,ccCompareGeneric-method |
| Class '"ccCompareResult"' | allAnnotation allAnnotation,ccCompareResult-method ccCompareResult ccCompareResult-class mainGraph mainGraph,ccCompareResult-method mainTable mainTable,ccCompareResult-method |
| Test data for 'categoryCompare' | ccData ccOpts ccResults ccResultsBPHier enrichLists geneLists gseaRes gUniverse table10 table48 |
| Perform annotation enrichment for multiple gene lists | ccEnrich ccEnrich,ccGeneList-method ccEnrich-method |
| Class "ccEnrichCollection" | ccEnrichCollection ccEnrichCollection-class graphType,ccEnrichCollection-method graphType<-,ccEnrichCollection-method minCount<-,ccEnrichCollection-method pvalueCutoff<-,ccEnrichCollection-method pvalueType<-,ccEnrichCollection-method |
| Class "ccEnrichResult" | ccEnrichResult ccEnrichResult-class fdr,ccEnrichResult-method GOccEnrichResult GOccEnrichResult-class graphType,ccEnrichResult-method graphType<-,ccEnrichResult-method KEGGccEnrichResult KEGGccEnrichResult-class minCount,ccEnrichResult-method minCount<-,ccEnrichResult-method pvalueCutoff,ccEnrichResult-method pvalueCutoff<-,ccEnrichResult-method pvalueType,ccEnrichResult-method pvalueType<-,ccEnrichResult-method [,ccEnrichResult,ANY,ANY,ANY-method [,ccEnrichResult,ANY,ANY-method |
| Class "ccGeneList" | ccGeneList ccGeneList-class ccType ccType,ccGeneList-method ccType<- ccType<-,ccGeneList-method fdr,ccGeneList-method fdr<-,ccGeneList-method listNames,ccGeneList-method pvalueCutoff,ccGeneList-method pvalueCutoff<-,ccGeneList-method testDirection,ccGeneList-method |
| Class "ccOptions" | ccOptions ccOptions-class compareColors compareColors,ccOptions-method compareColors<- compareColors<-,ccOptions-method compareIndx compareIndx,ccOptions-method compareNames compareNames,ccOptions-method compareNames<- compareNames<-,ccOptions-method cssClass cssClass,ccOptions-method listNames,ccOptions-method listNames<-,ccOptions-method outType outType,ccOptions-method outType<- outType<-,ccOptions-method |
| Methods for Function 'ccOutCyt' in Package 'categoryCompare' | ccOutCyt ccOutCyt,ccCompareResult,ccOptions-method ccOutCyt-methods |
| Class '"ccSigList"' | annotation,ccSigList-method category,ccSigList-method ccSigList ccSigList-class ontology,ccSigList-method sigID,ccSigList-method |
| Methods for Function 'cwReload' in Package 'categoryCompare' | cwReload cwReload,numeric,ccOptions-method cwReload,numeric,character,ccOptions-method cwReload-methods |
| Methods for Function 'cytOutData' | cytOutData cytOutData,list,ccCompareResult,mergedData-method cytOutData,list,ccCompareResult,missing-method cytOutData,list,missing,missing-method cytOutData-methods |
| Methods for Function 'cytOutNodes' | cytOutNodes cytOutNodes,character,numeric,list-method cytOutNodes,character,numeric,missing-method cytOutNodes-methods |
| Number of FDR runs to perform | fdr fdr<- |
| Class '"GENccEnrichResult"' | category,GENccEnrichResult-method ccCompareGeneric,GENccEnrichResult,ccOptions-method GENccEnrichResult GENccEnrichResult-class geneAnnMapping geneAnnMapping,GENccEnrichResult-method graphType,GENccEnrichResult-method graphType<-,GENccEnrichResult-method ontology,GENccEnrichResult-method sigID [,GENccEnrichResult,ANY,ANY,ANY-method [,GENccEnrichResult,ANY,ANY-method |
| Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion. | getAnnotation getGeneName getGeneSymbol getGO2ALLEGS getPATH2EG |
| graphType | graphType graphType-methods graphType<- |
| Class "HyperGParamsCC" | fdr,HyperGParamsCC-method fdr<-,HyperGParamsCC-method GOHyperGParams GOHyperGParams-class GOHyperGParamsCC GOHyperGParamsCC-class HyperGParamsCC HyperGParamsCC-class KEGGHyperGParams KEGGHyperGParams-class KEGGHyperGParamsCC KEGGHyperGParamsCC-class |
| Class "HyperGResultCC" | fdr,HyperGResultCC-method fdrvalues fdrvalues,HyperGResultCC-method fdrvalues-method GOHyperGResultCC GOHyperGResultCC-class HyperGResultCC HyperGResultCC-class KEGGHyperGResultCC KEGGHyperGResultCC-class minCount,HyperGResultCC-method minCount<-,HyperGResultCC-method pCC,HyperGResultCC-method pvalueCutoff<-,HyperGResultCC-method pvalueType,HyperGResultCC-method pvalueType<-,HyperGResultCC-method |
| Hypergeometric testing with false discovery rate | hyperGTestCC hyperGTestCC,HyperGParamsCC hyperGTestCC,HyperGParamsCC-method |
| listNames | listNames |
| Class '"mergedData"' | mergedData-class |
| Function 'mergeLists' in Package 'categoryCompare' | mergeLists mergeLists,ccGeneList,ccOptions-method mergeLists-methods |
| minCount | minCount minCount<- |
| Delete nodes with less than a certain number of genes annotated | minNodes minNodes,CytoscapeWindowClass,numeric-method |
| Type of p-values to return from object | pvalueType pvalueType<- |
| resetColors | resetColors resetColors,numeric,ccOptions-method resetColors-methods |
| Methods for Function show in Package `categoryCompare' | show,HyperGResultCC-method show-methods summary,HyperGResultCC-method summary-methods |
