NAMESPACE

# Generated by roxygen2: do not edit by hand

export(DsATAC.bam)
export(DsATAC.cellranger)
export(DsATAC.fragmentBed)
export(DsATAC.snakeATAC)
export(DsATACsc.archr)
export(DsATACsc.fragments)
export(DsNOMe.bisSNP)
export(cleanMem)
export(colZscores)
export(collapseMotifMatrix)
export(computeDiffAcc.rnb.nome)
export(fastqDirToTable)
export(findGroupMarkers)
export(findNearestGeneForGr)
export(findOrderedNames)
export(getATACfragments)
export(getComparisonInfo)
export(getConfigElement)
export(getConsensusPeakSet)
export(getGenomeObject)
export(getGroupsFromTable)
export(getJasparAnnot)
export(getMotifClustering)
export(getMotifDistMat)
export(getMotifOccurrences)
export(getNonOverlappingByScore)
export(getPeakSet.snakeATAC)
export(getSampleMetrics.snakeATAC)
export(getTfAnnot)
export(hmSeqLogo)
export(isCanonicalChrom)
export(loadConfig)
export(loadDsAcc)
export(prepareMotifmatchr)
export(projectMatrix_UMAP)
export(readMACS2peakFile)
export(rowZscores)
export(run_atac)
export(run_atac_chromvar)
export(run_atac_differential)
export(run_atac_exploratory)
export(run_atac_filtering)
export(run_atac_normalization)
export(run_atac_peakcalling)
export(run_atac_qc)
export(run_atac_sc_unsupervised)
export(safeMatrixStats)
export(saveConfig)
export(saveDsAcc)
export(setConfigElement)
export(smoothMagic)
exportClasses(DsATAC)
exportClasses(DsATACsc)
exportClasses(DsAcc)
exportClasses(DsNOMe)
exportMethods(addSampleAnnotCol)
exportMethods(aggregateRegionCounts)
exportMethods(callPeaks)
exportMethods(createReport_differential)
exportMethods(createReport_exploratory)
exportMethods(createReport_filtering)
exportMethods(createReport_normalization)
exportMethods(createReport_summary)
exportMethods(dimRed_UMAP)
exportMethods(exportCountTracks)
exportMethods(filterByGRanges)
exportMethods(filterCellsTssEnrichment)
exportMethods(filterChroms)
exportMethods(filterLowCovg)
exportMethods(getChromVarDev)
exportMethods(getCiceroGeneActivities)
exportMethods(getComparisonTable)
exportMethods(getCoord)
exportMethods(getCounts)
exportMethods(getCountsSE)
exportMethods(getCoverage)
exportMethods(getCovg)
exportMethods(getDESeq2Dataset)
exportMethods(getDiffAcc)
exportMethods(getFragmentGr)
exportMethods(getFragmentGrl)
exportMethods(getFragmentNum)
exportMethods(getGenome)
exportMethods(getInsertionKmerFreq)
exportMethods(getInsertionSites)
exportMethods(getMeth)
exportMethods(getMonocleCellDataSet)
exportMethods(getMotifEnrichment)
exportMethods(getMotifFootprints)
exportMethods(getNRegions)
exportMethods(getQuickTssEnrichment)
exportMethods(getRBFGeneActivities)
exportMethods(getRegionMapping)
exportMethods(getRegionTypes)
exportMethods(getSampleAnnot)
exportMethods(getSamples)
exportMethods(getScQcStatsTab)
exportMethods(getTssEnrichment)
exportMethods(getTssEnrichmentBatch)
exportMethods(iterativeLSI)
exportMethods(join)
exportMethods(maskMethNA)
exportMethods(mergePseudoBulk)
exportMethods(mergeSamples)
exportMethods(mergeStrands)
exportMethods(normalizeMeth)
exportMethods(plotInsertSizeDistribution)
exportMethods(regionAggregation)
exportMethods(regionSetCounts)
exportMethods(removeFragmentData)
exportMethods(removeRegionData)
exportMethods(removeRegionType)
exportMethods(removeRegions)
exportMethods(removeSamples)
exportMethods(samplePseudoBulk)
exportMethods(simulateDoublets)
exportMethods(transformCounts)
exportMethods(unsupervisedAnalysisSc)
import(GenomicAlignments)
import(GenomicRanges)
import(Matrix)
import(SummarizedExperiment)
import(ggplot2)
import(methods)
import(muLogR)
import(muRtools)
importFrom(GenomeInfoDb,"genome<-")
importFrom(GenomeInfoDb,"seqlengths<-")
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,genome)
importFrom(GenomeInfoDb,organism)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(IRanges,IRanges)
importFrom(IRanges,overlapsAny)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,elementNROWS)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,queryLength)
importFrom(S4Vectors,subjectHits)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(stats,as.dist)
importFrom(stats,as.formula)
importFrom(stats,as.hclust)
importFrom(stats,convolve)
importFrom(stats,cor)
importFrom(stats,cov)
importFrom(stats,dist)
importFrom(stats,ecdf)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,var)
importFrom(utils,combn)
importFrom(utils,data)
importFrom(utils,packageVersion)
importFrom(utils,read.table)
importFrom(utils,write.table)