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

importFrom("stats", "median")
importFrom("BiocGenerics", "unlist", "plotMA", "invertStrand")
importFrom("compiler", "cmpfun")
importFrom("deSolve", "ode")
importFrom("GenomicAlignments", "readGAlignmentPairs", "readGAlignments")
importFrom("GenomicFeatures","exonsBy","transcriptsBy","intronsByTranscript")
importFrom("GenomicRanges","reduce","seqnames","start","end","strand","width","findOverlaps")
importFrom("graphics", "abline", "axis", "image", "layout", "legend","matplot", "par", "points", "smoothScatter", "plot", "segments", "text", "title")
importFrom("grDevices", "colorRampPalette")
importFrom("IRanges", "IRanges", "psetdiff")
importFrom("preprocessCore", "normalize.quantiles")
importFrom("rootSolve", "multiroot")
importFrom("Rsamtools", "ScanBamParam")
importFrom("S4Vectors","subjectHits","queryHits","subjectLength","elementNROWS")
importFrom("stats", "approx", "dist", "ecdf", "hclust", "lm","na.omit", "optim", "optimize", "pchisq", "pnorm", "predict", "quantile", "rnorm", "runif", "splinefun", "uniroot", "p.adjust", "pt")
importFrom("utils", "capture.output", "read.table", "write.table", "head")

export("newINSPEcT", "runProcessingRateDelay", "runRNAdynamics", "compareSteadyNoNascent", 
	"quantifyExpressionsFromBAMs", "quantifyExpressionsFromTrCounts", "quantifyExpressionsFromTrAbundance")
exportMethods( "[", "AIC", "calculateDelta", "calculateTau", "chisqmodel", "chisqtest", "combine", 
    "compareSteady", "degradation", "dim", "featureNames", "featureNames<-", "geneClass", "getModel", 
    "getModel<-", "inHeatmap", "labeledSF", "logLik", "makeModelRates", "makeSimDataset", 
    "makeSimModel", "modelingParams", "modelingParams<-", "modelRates", "modelSelection", "modelSelection<-", 
    "nGenes", "nTpts", "plotGene", "plotMA", "processing", "processingDelay", "ratePvals", "ratesFirstGuess",
    "ratesFirstGuessVar", "removeModel", "rocCurve", "rocThresholds", "sfPlot", "show", "split", "synthesis", 
    "tpts", "viewModelRates")
exportClasses("INSPEcT", "INSPEcT_model", "INSPEcT_diffsteady")