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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(as_matrix)
export(bedToBigWig)
export(buildWindows)
export(calcConnections)
export(clusterBySNN)
export(countInsertions)
export(createPseudoBulk)
export(createPseudoBulkSummarizedExperiment)
export(featureToGR)
export(getCellNum)
export(getTssProfile)
export(getTxDbGenes)
export(grToFeature)
export(groupMeans)
export(groupSds)
export(insertionProfileSingles)
export(lsi)
export(makeCDS)
export(makeCicero)
export(mergePeak)
export(nonOverlappingGRanges)
export(plotTssProfile)
export(plot_GA_umap)
export(readFragments)
export(readInPeakNorm)
export(readSummits)
export(runMACS2)
export(summit2peak)
export(uniqueFeatures)
export(writeFragmentsToBed)
importFrom(AnnotationDbi,mapIds)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,subset)
importFrom(BiocGenerics,which)
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,coverage)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,tile)
importFrom(IRanges,IRanges)
importFrom(IRanges,Views)
importFrom(IRanges,subsetByOverlaps)
importFrom(IRanges,viewSums)
importFrom(Matrix,sparseMatrix)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,mcols)
importFrom(Seurat,FindClusters)
importFrom(Seurat,FindNeighbors)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(cicero,make_cicero_cds)
importFrom(data.table,fread)
importFrom(edgeR,cpm)
importFrom(ggplot2,aes)
importFrom(ggplot2,geom_hex)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(irlba,irlba)
importFrom(magrittr,"%>%")
importFrom(monocle3,detect_genes)
importFrom(monocle3,estimate_size_factors)
importFrom(monocle3,fData)
importFrom(monocle3,new_cell_data_set)
importFrom(rtracklayer,export.bw)
importFrom(stats,complete.cases)
importFrom(stringr,str_split)
importFrom(utils,txtProgressBar)
importFrom(viridis,scale_color_viridis)
importFrom(viridis,scale_fill_viridis)