NAMESPACE

export(interest, interest.sequential, InterestResult, getAnnotation, 
	addAnnotation, scaledRetention, referencePrepare, readInterestResults, 
	subInterestResult, mergeInterestResult, u12NbIndex, u12Index, 
	exactTestInterest, glmInterest, qlfInterest, treatInterest, 
	u12BoxplotNb, u12DensityPlot, u12DensityPlotIntron, lfc, getRepeatTable, 
	u12Boxplot, annotateU12, intexIndex, buildSsTypePwms, updateRowDataCol, 
	counts.InterestResults, plot.InterestResult, intexBoxplot, DEXSeqIntEREst,
	unionRefTr, interestResultIntEx, deseqInterest, psi)
exportMethods(counts, plot, boxplot)
import(graphics, grDevices, utils, grid, methods, SummarizedExperiment)
importFrom(Biostrings, getSeq, matchPWM, PWM, unitScale, reverseComplement, 
	DNAString)
importFrom(BiocGenerics, counts)
importFrom(seqinr, read.fasta, getSequence, getFrag)
importFrom(seqLogo, seqLogo)
importFrom(IRanges, IRanges)
importFrom(stats, density, loess.smooth, cor, median, model.matrix)
importFrom(S4Vectors, queryHits, subjectHits, metadata)
importFrom(edgeR, DGEList, estimateDisp, estimateExonGenewiseDisp, exactTest, 
	topTags, estimateGLMTagwiseDisp, estimateGLMTrendedDisp, 
	estimateGLMCommonDisp, glmFit, glmLRT, glmQLFit, glmQLFTest, glmTreat)
importFrom(GenomicFeatures, DEFAULT_CIRC_SEQS, makeTxDbFromUCSC, 
	makeTxDbFromBiomart, makeTxDbFromGFF, exonsBy, transcriptsBy, 
	intronsByTranscript)
importFrom(GenomicRanges, seqnames, start, end, width, strand, ranges, GRanges, 
	findOverlaps, reduce, gaps)
importFrom(Rsamtools, BamFile, ScanBamParam, scanBamFlag, scanBamWhat, isOpen)
importFrom(DBI, dbConnect, dbSendQuery, dbGetQuery, dbDisconnect)
importFrom(RMySQL, MySQL)
importFrom(BiocParallel, SerialParam, MulticoreParam, bpiterate)
importFrom(GenomicAlignments, readGAlignmentPairs, readGAlignmentsList)
importFrom(DEXSeq, DEXSeqDataSet, DEXSeq)
importFrom(DESeq2, DESeqDataSetFromMatrix, sizeFactors, DESeq, results)