Basic4Cseq
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

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Vignettes
Functions
111
Source code
20
Man pages
22
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Basic4Cseq: Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
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API for Basic4Cseq
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Global functions
.basic4CPlot Source code
.checkRestrictionEnzymeSequence Source code
.chooseNearCisFragments Source code
.createVirtualFragmentLibraryMain Source code
.createVirtualFragmentLibrary_BSgenome Source code
.createVirtualFragmentLibrary_DNAString Source code
.drawDigestionFragmentHistogram Source code
.drawHeatmapMain Source code
.drawHeatmap_Data4Cseq Source code
.drawHeatmap_DataFrame Source code
.drawMetaData Source code
.exportVisualizationFragmentData Source code
.formatFragmentDataMain Source code
.formatFragmentData_Data4Cseq Source code
.formatFragmentData_DataFrame Source code
.getReadDistribution Source code
.giveEnzymeSequence Source code
.giveWigDataChromosome Source code
.importVisualizationFragmentData Source code
.normalizeFragmentData Source code
.plotTransInteractionsMain Source code
.plotTransInteractions_Character Source code
.plotTransInteractions_DataFrame Source code
.prepare4CseqData Source code
.printBEDFragmentLibrary Source code
.printWigFile Source code
.readPointsOfInterestFile Source code
.readsToFragments Source code
.simulateDigestionChromosome_DNAString Source code
.simulateDigestionChromosome_MaskedDNAString Source code
.simulateDigestion_BSgenome Source code
.simulateDigestion_Character Source code
.splitChromosome_DNAString Source code
.visualizeViewpointMain Source code
.visualizeViewpoint_Data4Cseq Source code
.visualizeViewpoint_DataFrame Source code
Data4Cseq Man page
Data4Cseq,character,numeric,numeric,data.frame,GAlignments-metho Man page
Data4Cseq,character,numeric,numeric,missing,missing-method Man page
Data4Cseq-class Man page
checkRestrictionEnzymeSequence Man page
checkRestrictionEnzymeSequence,character,character-method Man page
chooseNearCisFragments Man page
chooseNearCisFragments,Data4Cseq,numeric-method Man page
createVirtualFragmentLibrary Man page
createVirtualFragmentLibrary,BSgenome,character,character,numeri Man page
createVirtualFragmentLibrary,DNAString,character,character,numer Man page
drawDigestionFragmentHistogram Man page
drawDigestionFragmentHistogram,data.frame-method Man page
drawHeatmap Man page
drawHeatmap,Data4Cseq-method Man page
drawHeatmap,data.frame-method Man page
exportVisualizationFragmentData Man page
exportVisualizationFragmentData,Data4Cseq,character-method Man page
getReadDistribution Man page
getReadDistribution,Data4Cseq-method Man page
giveEnzymeSequence Man page
giveEnzymeSequence,character,character-method Man page
importVisualizationFragmentData Man page
importVisualizationFragmentData,character-method Man page
liverData Man page
liverDataRaw Man page
nearCisFragments Man page
nearCisFragments,Data4Cseq-method Man page
nearCisFragments<- Man page
nearCisFragments<-,Data4Cseq,data.frame-method Man page
normalizeFragmentData Man page
normalizeFragmentData,Data4Cseq-method Man page
plotTransInteractions Man page
plotTransInteractions,character,character,numeric,character-meth Man page
plotTransInteractions,data.frame,character,numeric,data.frame-me Man page
pointsOfInterest Man page
pointsOfInterest,Data4Cseq-method Man page
pointsOfInterest<- Man page
pointsOfInterest<-,Data4Cseq,data.frame-method Man page
prepare4CseqData Man page
prepare4CseqData,character,character,character,character-method Man page
printBEDFragmentLibrary Man page
printBEDFragmentLibrary,character,character-method Man page
printWigFile Man page
printWigFile,Data4Cseq-method Man page
rawFragments Man page
rawFragments,Data4Cseq-method Man page
rawFragments<- Man page
rawFragments<-,Data4Cseq,data.frame-method Man page
rawReads Man page
rawReads,Data4Cseq-method Man page
rawReads<- Man page
rawReads<-,Data4Cseq,GAlignments-method Man page
readLength Man page
readLength,Data4Cseq-method Man page
readLength<- Man page
readLength<-,Data4Cseq,numeric-method Man page
readPointsOfInterestFile Man page
readPointsOfInterestFile,character-method Man page
readsToFragments Man page
readsToFragments,Data4Cseq,character-method Man page
simulateDigestion Man page
simulateDigestion,character,character,BSgenome-method Man page
simulateDigestion,character,character,character-method Man page
viewpointChromosome Man page
viewpointChromosome,Data4Cseq-method Man page
viewpointChromosome<- Man page
viewpointChromosome<-,Data4Cseq,character-method Man page
viewpointInterval Man page
viewpointInterval,Data4Cseq-method Man page
viewpointInterval<- Man page
viewpointInterval<-,Data4Cseq,numeric-method Man page
visualizeViewpoint Man page
visualizeViewpoint,Data4Cseq-method Man page
visualizeViewpoint,data.frame-method Man page
Basic4Cseq documentation built on Nov. 8, 2020, 6:53 p.m.

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