# Generated by roxygen2: do not edit by hand

export(annoSeqlogo)
export(bin)
export(calcBinnedKmerEnr)
export(calcBinnedMotifEnrHomer)
export(calcBinnedMotifEnrR)
export(dumpJaspar)
export(findHomer)
export(findMotifHits)
export(getColsByBin)
export(getKmerFreq)
export(getZeroBin)
export(homerToPFMatrixList)
export(motifKmerSimilarity)
export(motifSimilarity)
export(parseHomerOutput)
export(plotBinDensity)
export(plotBinDiagnostics)
export(plotBinHist)
export(plotBinScatter)
export(plotMotifHeatmaps)
export(plotSelectionProb)
export(plotStabilityPaths)
export(prepareHomer)
export(randLassoStabSel)
export(sampleRandomRegions)
export(seqLogoGrob)
export(setZeroBin)
importFrom(BSgenome,getSeq)
importFrom(BiocGenerics,sort)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,width)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpnworkers)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,DNA_ALPHABET)
importFrom(Biostrings,DNA_BASES)
importFrom(Biostrings,alphabetFrequency)
importFrom(Biostrings,fasta.seqlengths)
importFrom(Biostrings,matchPWM)
importFrom(Biostrings,oligonucleotideFrequency)
importFrom(Biostrings,reverseComplement)
importFrom(ComplexHeatmap,AnnotationFunction)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,add_heatmap)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(ComplexHeatmap,subset_gp)
importFrom(GenomicRanges,"end<-")
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,sort)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,width)
importFrom(IRanges,IRanges)
importFrom(IRanges,start)
importFrom(IRanges,width)
importFrom(RSQLite,SQLite)
importFrom(RSQLite,dbConnect)
importFrom(RSQLite,dbDisconnect)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,isEmpty)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,split)
importFrom(S4Vectors,subjectHits)
importFrom(Seqinfo,seqlengths)
importFrom(Seqinfo,seqlevels)
importFrom(Seqinfo,seqnames)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(TFBSTools,ID)
importFrom(TFBSTools,Matrix)
importFrom(TFBSTools,PFMatrix)
importFrom(TFBSTools,PFMatrixList)
importFrom(TFBSTools,PWMatrix)
importFrom(TFBSTools,PWMatrixList)
importFrom(TFBSTools,getMatrixSet)
importFrom(TFBSTools,name)
importFrom(TFBSTools,toPWM)
importFrom(XVector,subseq)
importFrom(circlize,colorRamp2)
importFrom(cli,cli_abort)
importFrom(cli,cli_alert_info)
importFrom(cli,cli_inform)
importFrom(cli,cli_progress_step)
importFrom(cli,cli_warn)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,geom_area)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rug)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,ylim)
importFrom(glmnet,glmnet)
importFrom(glmnet,predict.glmnet)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grid,gpar)
importFrom(grid,grid.draw)
importFrom(grid,grid.rect)
importFrom(grid,polygonGrob)
importFrom(grid,popViewport)
importFrom(grid,pushViewport)
importFrom(grid,unit)
importFrom(grid,viewport)
importFrom(methods,.valueClassTest)
importFrom(methods,as)
importFrom(methods,existsMethod)
importFrom(methods,formalArgs)
importFrom(methods,is)
importFrom(methods,show)
importFrom(rlang,.data)
importFrom(stabs,stabsel)
importFrom(stats,cor)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,pbinom)
importFrom(stats,ppois)
importFrom(stats,quantile)
importFrom(stats,reorder)
importFrom(stats,runif)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,starts_with)
importFrom(tools,file_path_as_absolute)
importFrom(utils,getFromNamespace)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,strcapture)
importFrom(utils,write.table)
