export(align_to_unip)
export(calculate_boundary)
export(DominoEffect)
export(identify_hotspots)
export(import_txdb)
export(map_to_func_elem)
export(GPo_of_hotspots)

importClassesFrom(VariantAnnotation, CollapsedVCF)
importClassesFrom(Biostrings, AAString)
importClassesFrom(GenomicRanges, GPos)

importFrom(utils, read.table, write.table, download.file, read.delim)
importFrom(utils, txtProgressBar, setTxtProgressBar)
importFrom(stats, aggregate, dbinom, p.adjust)
importFrom(biomaRt, useMart, getBM, getSequence, exportFASTA, listDatasets)
importFrom(Biostrings, readAAStringSet, width, AAString, subseq, pairwiseAlignment)
importFrom(Biostrings, subseq, countPattern, matchPattern, subject, pattern, pid, start, nchar)

importFrom(data.table, setkey)
importFrom(data.table, data.table)
importFrom(data.table, fread)

importFrom(stats, ppois, end)
importFrom(utils, data, head)

importFrom(VariantAnnotation, info, readVcf)
importFrom(GenomeInfoDb, seqnames)
importFrom(AnnotationDbi, select, keys)
importFrom(SummarizedExperiment, rowRanges)
importFrom(IRanges, ranges)
importFrom(GenomicRanges, GPos, mcols, pos)

importFrom(methods, is)