importFrom("limma", normalizeBetweenArrays, lmFit, eBayes, topTable)

importFrom("DESeq2", rlog, vst, DESeq, results, DESeqDataSetFromMatrix)

importFrom("DESeq2", rlog, vst, varianceStabilizingTransformation, DESeq, results, DESeqDataSetFromMatrix)

# MapReduce, gather, and lapply functions

useDynLib( "DSL" , .registration = TRUE )

importFrom("graphics", "axis", "lines", "plot", "points", "symbols", "par", "text")
importFrom("stats", "cor", "median", "qchisq", "quantile", "sd", "qnorm")

importFrom("graphics", "filled.contour", "image", "par", "persp",

importFrom("graphics", "filled.contour", "image", "par", "persp", "plot", "segments")
importFrom("stats", "dnorm", "integrate", "rnorm", "runif", "sd", "var")

importFrom("stats", "pchisq", "pnorm", "quantile", "rbinom", "rexp", "rnorm", "runif")

importFrom("stats", "coef", "lm", "predict", "rbinom", "rnorm")
export(sim_Kstage, ql, owl, predict.ql, predict.owl)

importFrom("stats", "as.formula", "binomial", "fitted", "get_all_vars",
"glm", "lm", "lowess", "model.frame", "model.matrix",

importFrom("graphics", "abline", "hist", "plot", "points")
"model.response", "qnorm", "quantile", "rbinom", "rnorm",

importFrom(ggplot2, ggplot, aes_string, geom_point, geom_line, ggtitle, ggsave)
importFrom(ggplot2, coord_cartesian, annotation_custom, theme_bw, xlab, ylab)
importFrom(grid, gpar, segmentsGrob, arrow, unit, grobTree)

#importFrom(utils, read.table, read.csv, write.table, glob2rx, head, tail, file_test, unzip, choose.dir, choose.files, Filter)

importFrom(ggplot2, ggplot, aes_string, geom_point, geom_line, geom_ribbon, ggtitle, ggsave)
importFrom(ggplot2, coord_cartesian, annotation_custom, theme, theme_bw, xlab, ylab)
importFrom(ggplot2, facet_grid, scale_shape_manual, guides, guide_legend, expand_limits)

importFrom(ggplot2, scale_shape_manual, scale_y_continuous, guides, guide_legend, expand_limits)

importFrom("stats", "fitted", "na.omit", "predict", "terms")

importFrom("stats", "coef", "contrasts", "dgeom", "glm", "logLik","model.matrix", "model.response", "quasipoisson", "runif")