# Generated by roxygen2: do not edit by hand

export(addEnsemblAnnotation)
export(annotateEvents)
export(callPrimer3)
export(checkPrimer)
export(eventOutcomeCompare)
export(eventOutcomeTranslate)
export(eventPlot)
export(extendROI)
export(extractSpliceEvents)
export(extractSpliceSites)
export(findCompatibleEvents)
export(findCompatibleExon)
export(findTX)
export(getPCRsizes)
export(getRegionDNA)
export(insertRegion)
export(makeROI)
export(makeUniqueIDs)
export(plot_seqlogo)
export(psiPlot)
export(removeRegion)
export(shapiroAcceptor)
export(shapiroDensity)
export(shapiroDonor)
export(splitPCRhit)
import(BSgenome.Mmusculus.UCSC.mm9)
import(Seqinfo)
import(GenomicAlignments)
import(GenomicFeatures)
import(GenomicRanges)
import(Gviz)
import(IRanges)
import(S4Vectors)
import(biomaRt)
import(ggplot2)
import(googleVis)
import(grDevices)
import(graphics)
import(seqLogo)
import(stringr)
importFrom(Biostrings,AA_ALPHABET)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,PWMscoreStartingAt)
importFrom(Biostrings,consensusMatrix)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,matchPattern)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,startIndex)
importFrom(Biostrings,subseq)
importFrom(Biostrings,translate)
importFrom(Biostrings,vmatchPattern)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,elementNROWS)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(methods,is)
importFrom(plyr,ldply)
importFrom(pwalign,aligned)
importFrom(pwalign,deletion)
importFrom(pwalign,indel)
importFrom(pwalign,insertion)
importFrom(pwalign,mismatchTable)
importFrom(pwalign,nmismatch)
importFrom(pwalign,pairwiseAlignment)
importFrom(pwalign,pattern)
importFrom(pwalign,subject)
importFrom(pwalign,unaligned)
importFrom(utils,read.delim)
importFrom(utils,read.table)
