NAMESPACE

import(ggplot2)

importFrom(bio3d, read.pdb, pdbseq)
importFrom(rlog, log_info)
importFrom(dplyr, intersect, "%>%", "reframe", "group_by", "pull", "mutate")
importFrom(comprehenr, to_list)
importFrom(RColorBrewer, brewer.pal)
importFrom(scales, col_bin)
importFrom(NGLVieweR, stageParameters,
           addRepresentation,
           setQuality)
importFrom("grDevices", "colorRamp", "colorRampPalette")
importFrom(S4Vectors, DataFrame)
importFrom("graphics", "image")
    importFrom("methods", "is", "new")
    importFrom("stats", "C", "approxfun", "coef", "complete.cases",
               "dbeta", "dgamma", "dlnorm", "dnorm", "dpois",
               "nls.control", "predict", "quantile", "rbeta", "rgamma",
               "rnorm", "runif", "na.omit","stepfun", "prcomp")
importFrom("minpack.lm", "nlsLM", "nls.lm.control")
importFrom("BiocParallel", "bplapply", "bpparam")
importFrom("LaplacesDemon", "dlaplace", "rlaplace")
importFrom("MASS", "fitdistr", "ginv")
importFrom("genlasso", "trendfilter", "cv.trendfilter")
importFrom("Biobase", "validMsg")
importFrom("coda", "gelman.diag", "as.mcmc.list", "as.mcmc")
importFrom("matrixStats", "colProds")
importFrom("pheatmap", "pheatmap")
importFrom("dbplyr", "sql")
importFrom("vegan", "procrustes")
importFrom("plyr", "ldply")
importFrom("ropls", "opls")
importFrom("tidyr", "pivot_wider", "pivot_longer")
importFrom("stringr", "str_count", "str_sub")
importFrom("utils", "setTxtProgressBar", "txtProgressBar")

exportClasses("RexChains",
              "RexSummary",
              "RexParams",
              "RexChain",
              "RexDifferential")

exportMethods("posteriorEstimates",
              "Rex.quantiles",
              "Rex.resolution",
              "Rex.peptideError",
              "Rex.globals",
              "Rex.predictionError",
              "Rex.estimates",
              "Rex.probs",
              "Rex.eFDR")

export(prepareIndexes,
       maxUptakes,
       coverageHeatmap,
       cleanHDX,
       cleanLong,
       doublelogisticFunction,
       logisticFunction,
       processDifferential,
       EFDR,
       processTREuncertainty,
       rex,
       RexProcess,
       uptakeGuess,
       define_color_function,
       hdx_to_pdb_colours,
       view_structure,
       plotVolcano,
       plotButterfly,
       plotTimeAveragedButterfly,
       plotSigma,
       plotLogLikelihoods,
       plotPeptideError,
       plotResidueResolution,
       UnsupervisedCSA,
       plotUCSA,
       supervisedCSA,
       plotSCSA,
       plotLoadingSCSA,
       sampleTREuncertainty,
       plotTREuncertainty,
       plotTREuncertaintyLoadings,
       uptakePredict,
       plotUptake,
       marginalEffect,
       plotUptakeUncertainty)