# Generated by roxygen2: do not edit by hand

export(calculatePvalue)
export(exportMBbed)
export(exportMBtable)
export(findSupportingRemapPeaks)
export(motifbreakR)
export(plotMB)
export(shiny_motifbreakR)
export(snps.from.file)
export(snps.from.rsid)
export(variants.from.file)
import(BiocGenerics)
import(BiocParallel)
import(GenomeInfoDb)
import(GenomicRanges)
import(IRanges)
import(S4Vectors)
import(bsicons)
import(bslib)
import(grDevices)
import(methods)
import(parallel)
import(shiny)
importClassesFrom(motifStack,marker)
importClassesFrom(motifStack,pfm)
importFrom(BSgenome,available.genomes)
importFrom(BSgenome,snplocs)
importFrom(BSgenome,snpsById)
importFrom(BSgenome,snpsByOverlaps)
importFrom(BiocFileCache,BiocFileCache)
importFrom(BiocFileCache,bfcadd)
importFrom(BiocFileCache,bfcdownload)
importFrom(BiocFileCache,bfcneedsupdate)
importFrom(BiocFileCache,bfcnew)
importFrom(BiocFileCache,bfcquery)
importFrom(BiocFileCache,bfcrpath)
importFrom(BiocParallel,bplapply)
importFrom(Biostrings,BStringSetList)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,DNAStringSetList)
importFrom(Biostrings,DNA_ALPHABET)
importFrom(Biostrings,IUPAC_CODE_MAP)
importFrom(Biostrings,complement)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,matchPattern)
importFrom(Biostrings,replaceAt)
importFrom(Biostrings,replaceLetterAt)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,uniqueLetters)
importFrom(DT,DTOutput)
importFrom(DT,JS)
importFrom(DT,datatable)
importFrom(DT,formatRound)
importFrom(DT,renderDT)
importFrom(Gviz,AnnotationTrack)
importFrom(Gviz,GenomeAxisTrack)
importFrom(Gviz,HighlightTrack)
importFrom(Gviz,IdeogramTrack)
importFrom(Gviz,SequenceTrack)
importFrom(Gviz,plotTracks)
importFrom(SummarizedExperiment,rowRanges)
importFrom(TFMPvalue,TFMpv2sc)
importFrom(TFMPvalue,TFMsc2pv)
importFrom(VariantAnnotation,ScanVcfParam)
importFrom(VariantAnnotation,VcfFile)
importFrom(VariantAnnotation,alt)
importFrom(VariantAnnotation,isSNV)
importFrom(VariantAnnotation,readVcf)
importFrom(VariantAnnotation,ref)
importFrom(biomaRt,getBM)
importFrom(biomaRt,searchDatasets)
importFrom(biomaRt,useEnsembl)
importFrom(grid,gpar)
importFrom(grid,grid.newpage)
importFrom(grid,popViewport)
importFrom(grid,pushViewport)
importFrom(grid,viewport)
importFrom(matrixStats,colMaxs)
importFrom(matrixStats,colMins)
importFrom(matrixStats,colRanges)
importFrom(motifStack,DNAmotifAlignment)
importFrom(motifStack,addBlank)
importFrom(motifStack,colorset)
importFrom(motifStack,motifStack)
importFrom(motifStack,plotMotifLogo)
importFrom(motifStack,plotMotifLogoStack)
importFrom(parallel,clusterEvalQ)
importFrom(pwalign,deletion)
importFrom(pwalign,insertion)
importFrom(pwalign,pairwiseAlignment)
importFrom(rtracklayer,export.bed)
importFrom(rtracklayer,import)
importFrom(stringr,str_extract)
importFrom(stringr,str_length)
importFrom(stringr,str_locate_all)
importFrom(stringr,str_pad)
importFrom(stringr,str_replace)
importFrom(stringr,str_sort)
importFrom(stringr,str_split)
importFrom(stringr,str_sub)
importFrom(stringr,str_trim)
importFrom(tools,R_user_dir)
importFrom(utils,write.csv)
importFrom(utils,write.table)
importFrom(vroom,vroom)
