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128 lines (127 loc) · 3.29 KB
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# Generated by roxygen2: do not edit by hand
export(DEtables)
export(PromoterShift)
export(TAGtables)
export(TSSmatrix)
export(TSSr)
export(annotateCluster)
export(assignedClusters)
export(callEnhancer)
export(clusterShape)
export(clusterTSS)
export(consensusCluster)
export(consensusClusters)
export(deGene)
export(enhancers)
export(exportClustersTable)
export(exportClustersToBed)
export(exportDETable)
export(exportEnhancerTable)
export(exportShapeTable)
export(exportShiftTable)
export(exportTSStable)
export(exportTSStoBedgraph)
export(filterTSS)
export(filteredClusters)
export(getTSS)
export(librarySizes)
export(mergeSamples)
export(normalizeTSS)
export(plotCorrelation)
export(plotDE)
export(plotInterQuantile)
export(plotShape)
export(plotTSS)
export(plotTssPCA)
export(refTable)
export(shapeCluster)
export(shiftPromoter)
export(tagClusters)
export(unassignedClusters)
exportClasses(TSSr)
exportMethods(DEtables)
exportMethods(PromoterShift)
exportMethods(TAGtables)
exportMethods(TSSmatrix)
exportMethods(annotateCluster)
exportMethods(assignedClusters)
exportMethods(callEnhancer)
exportMethods(clusterShape)
exportMethods(clusterTSS)
exportMethods(consensusCluster)
exportMethods(consensusClusters)
exportMethods(deGene)
exportMethods(enhancers)
exportMethods(exportClustersTable)
exportMethods(exportClustersToBed)
exportMethods(exportDETable)
exportMethods(exportEnhancerTable)
exportMethods(exportShapeTable)
exportMethods(exportShiftTable)
exportMethods(exportTSStable)
exportMethods(exportTSStoBedgraph)
exportMethods(filterTSS)
exportMethods(filteredClusters)
exportMethods(getTSS)
exportMethods(librarySizes)
exportMethods(mergeSamples)
exportMethods(normalizeTSS)
exportMethods(plotCorrelation)
exportMethods(plotDE)
exportMethods(plotInterQuantile)
exportMethods(plotShape)
exportMethods(plotTSS)
exportMethods(plotTssPCA)
exportMethods(refTable)
exportMethods(shapeCluster)
exportMethods(shiftPromoter)
exportMethods(show)
exportMethods(tagClusters)
exportMethods(unassignedClusters)
import(GenomeInfoDb)
import(data.table)
import(ggplot2)
import(parallel)
import(rtracklayer)
import(stringr)
importFrom(BiocGenerics,union)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,elementMetadata)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,resize)
importFrom(IRanges,IRanges)
importFrom(IRanges,findOverlaps)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,bamFlag)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(dplyr,filter)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,rainbow)
importFrom(graphics,hist)
importFrom(graphics,pairs)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(methods,as)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,setRefClass)
importFrom(stats,chisq.test)
importFrom(stats,cor)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stats,qpois)
importFrom(txdbmaker,makeTxDbFromGFF)
importFrom(utils,installed.packages)
importFrom(utils,read.table)
importFrom(utils,write.table)