NAMESPACE

import("SingleCellExperiment")

importMethodsFrom("IRanges", extractList, subsetByOverlaps)
importMethodsFrom("GenomeInfoDb", seqlevels, "seqlevels<-", seqnames)
importFrom("GenomeInfoDb", orderSeqlevels)

importFrom("grDevices", "col2rgb", "dev.off", "grey", "gray", "png", "rgb")
importFrom("graphics", "abline", "axis", "barplot", "boxplot", "legend", "mtext", 
    "par", "plot", "rect", "segments", "symbols", "text")
importFrom("methods", "as", "is")
importFrom("stats", "chisq.test", "cor", "cor.test", "formula", "lm", "mad", "median", 
    "model.matrix", "p.adjust", "pchisq", "phyper", "pnorm", "qnorm","quantile", 
    "rnorm", "runif", "var")
importFrom("utils", "available.packages", "browseURL", "capture.output", 
    "download.file", "data", "head", "memory.limit", "read.csv", "read.delim", 
    "tail", "untar", "unzip", "write.table")

export( 
    analyzeCancerType,
    analyzeCooccurence,
    analyzeStrata,
    annoCellType,
    annotateCytoBands,
    bpCrossType,
    bpCyclins,
    bpSubtypeStrata,
    bpType,
    circosSubtypeAssociation,
    compileMarkers,
    corPermTest,
    extendObservations,
    facetTumors,
    generateInferCNVInput,
    getBroadSubtypes,
    getCelltypeSubtypeMatrix,
    getCellAnnotation,
    getClassifierGenes,
    getClassProbs,
    getCnvGenesFromTCGA,
    getCommonMarkers, 
    getExtendedVerhaakSignature,
    getMatchedAbsoluteCalls,
    getPerc,
    getRecurrentDriverGenes,
    ggplotSubtypeStrata,
    gistic2RSE,
    mapOVSubtypes,
    margin,
    markerHeatmap,
    markerHeatmapList,
    matrixPlot,
    plotCommonSCNAs,
    plotCorrelation,
    plotMainCellTypes,
    plotNrCNAsPerSubtype,
    plotNrSamples,
    plotNrSubtypesVsNrGisticRegions,
    plotPurityStrata,
    plotSubclonalityDistributions,
    plotSubtypePurityPloidy,
    plotType,
    plotlyPie,
    populationRanges,
    populationRangesRO,
    preprocessSCE,
    pseudotimeHeatmap,
    querySubclonality,
    readObservations,
    scHeatmap,
    scHeatmap2,
    stratifyByPurity,
    stratifySubclonality,
    subsetByCellType,
    subsetObservations,
    symbols2ranges,
    testSubtypes,
    tissueScore,
    transferCellType,
    volcanoCorrelation     
)