import("methods","Biobase","BiocParallel","pROC", "DESeq2","plgem","SummarizedExperiment","TxDb.Mmusculus.UCSC.mm9.knownGene","shiny")

importFrom("stats", "median", "constrOptim", "cor", "qchisq", "sd")
importFrom("BiocGenerics", "unlist", "plotMA", "invertStrand")
importFrom("deSolve", "ode")
importFrom("readxl", "read_excel")
importFrom("GenomicAlignments", "readGAlignmentPairs", "readGAlignments")
importFrom("GenomicFeatures","exonsBy","transcriptsBy","intronsByTranscript")
importFrom("GenomicRanges","reduce","seqnames","start","end","strand","width","findOverlaps")
importFrom("Seqinfo","seqlengths","seqlevels","seqlevels<-")
importFrom("graphics", "abline", "axis", "image", "layout", "legend","matplot", "matlines", "mtext", "par", "points", "smoothScatter", "plot", "segments", "text", "title")
importFrom("grDevices", "colorRampPalette", "dev.off", "pdf", "densCols")
importFrom("IRanges", "IRanges", "psetdiff", "Views")
importFrom("rootSolve", "multiroot")
importFrom("Rsamtools", "ScanBamParam")
importFrom("S4Vectors","subjectHits","queryHits","subjectLength","elementNROWS")
importFrom("stats", "approx", "density", "dist", "ecdf", "hclust", "lm","na.omit", "optim", "optimize", "pchisq", "pnorm", "predict", "quantile", "rnorm", "runif", "splinefun", "uniroot", "p.adjust", "pt")
importFrom("utils", "capture.output", "read.csv", "read.table", "write.table", "head", "tail", "str")
importFrom("KernSmooth", "bkde2D")
importFrom("rtracklayer", "import")

export("newINSPEcT", "runINSPEcTGUI", "inspectFromBAM", "inspectFromPCR",
    "quantifyExpressionsFromBAMs", "quantifyExpressionsFromBWs", "quantifyExpressionsFromTrCounts", 
    "quantifyExpressionsFromTrAbundance")
exportMethods( "[", "AIC", "calculateDelta", "calculateRatePvals", "calculateTau", "chisqmodel", "chisqtest", "combine",
    "compareSteady", "computeConfidenceIntervals", "convergence", "correlationPlot", "degradation", "dim", "featureNames", 
    "featureNames<-", "geneClass", "inHeatmap", "labeledSF", "logLik", "makeModelRates", "makeOscillatorySimModel", 
    "makeSimDataset", "makeSimModel", "modelingParams", "modelRates", "modelRatesNF", "modelSelection", 
    "nGenes", "nTpts", "plotGene", "plotMA", "processing", "processingDelay", "ratePvals", 
    "ratesFirstGuess","ratesFirstGuessVar", "removeModel", "rocCurve", "rocThresholds", "show", "split", "synthesis", 
    "tpts", "viewConfidenceIntervals", "viewModelRates", "premature", "mature", "PTratio", "PTreg", "plotPMtrend", "plotPMgene",
    "compareSteadyNoNascent")
exportClasses("INSPEcT", "INSPEcT_model", "INSPEcT_diffsteady", "INSPEcT_steadyNoNascent")
