NAMESPACE
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 ##
 ## Importing
 ##
 
 import(methods)
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 import(S4Vectors)
 import(IRanges)
 import(GenomicRanges)
 import(SummarizedExperiment)
 import(DelayedArray)
 import(HDF5Array)
 import(BiocParallel)
 import(limma)
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 importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",
            "combine", "density", "intersect", "lapply", "ncol",
            "nrow", "order", "paste", "pmax", "pmin", "rbind",
            "Reduce", "rep.int", "rownames", "sapply", "setdiff",
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            "strand", "strand<-", "union", "unique", "updateObject", "unstrand")
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 importFrom(stats, "approxfun", "fisher.test", "ppoints",
            "predict", "preplot", "qchisq",
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            "qqplot", "qunif", "cov2cor",
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            "setNames")
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 importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
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            "mtext", "par", "plot", "points", "polygon", "rect", "rug", "text")
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 import(parallel)
 importFrom(locfit, "locfit", "lp")
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 importFrom(DelayedMatrixStats, "rowSds", "rowVars", "colMeans2", "colSums2",
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            "rowSums2", "rowMeans2", "rowAlls")
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 importFrom(scales, "alpha")
 importClassesFrom(Biobase, "AnnotatedDataFrame")
 importMethodsFrom(Biobase, "annotatedDataFrameFrom",
                   "pData", "pData<-",
                   "sampleNames", "sampleNames<-")
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 importFrom(Biobase, "validMsg")
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 importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo",
                   "seqinfo<-", "seqnames", "seqnames<-", "seqlevels",
                   "seqlevels<-", "sortSeqlevels")
 importFrom(GenomeInfoDb, "Seqinfo")
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 importFrom(gtools, "combinations")
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 importFrom(Rcpp, sourceCpp)
 
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 # NOTE: data.table has some NAMESPACE clashes with functions in Bioconductor,
 #       e.g., shift(). If new ones are discovered, add them to this list.
 import(data.table, except = c(shift, first, second))
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 importFrom(permute, "shuffleSet", "how")
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 importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement")
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 importFrom(utils, "read.delim")
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 importFrom(BSgenome, "vmatchPattern")
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 importFrom(tools, "file_path_as_absolute")
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 importFrom(R.utils, "isGzipped", "isBzipped", "gunzip", "bunzip2")
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 ##
 ## Exporting
 ##
 
 exportClasses("hasGRanges",
               "BSseq",
               "BSseqTstat",
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               "BSseqStat",
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               "matrixOrNULL")
 
 exportMethods("[", "show",
               "seqnames", "seqnames<-",
               "seqlevels", "seqlevels<-",
               "seqlengths", "seqlengths<-",
               "start", "start<-",
               "end", "end<-",
               "width", "width<-",
               "strand", "strand<-",
               "granges",
               "dim", "nrow", "ncol",
               "sampleNames", "sampleNames<-",
               "pData", "pData<-",
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               "findOverlaps", "overlapsAny", "subsetByOverlaps",
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               "combine", "updateObject")
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 export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
        "collapseBSseq", "orderBSseq", "hasBeenSmoothed", "chrSelectBSseq",
        "BSmooth", "BSmooth.tstat", "dmrFinder", "fisherTests",
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        "combineList", "strandCollapse",
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        "plotRegion", "plotManyRegions",
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        "read.umtab", "read.umtab2", "read.bsmooth", "read.bismark",
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        "poissonGoodnessOfFit", "binomialGoodnessOfFit",
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        "data.frame2GRanges", "BSseqTstat",
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        "BSseqStat",
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        "findLoci")
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 S3method("print", "chisqGoodnessOfFit")
 S3method("plot", "chisqGoodnessOfFit")
 S3method("print", "summary.BSseqTstat")
 S3method("summary", "BSseqTstat")
 S3method("plot", "BSseqTstat")
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 ## Fixes, to be removed
 
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 exportMethods("assays", "assayNames")
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 # C++ code registration
 useDynLib(bsseq, .registration = TRUE, .fixes = "cxx_")