export( loadMAdata, runQC, extractFactors, diffExp, polarPlot, loadGSC, runGSA, GSAsummaryTable, geneSetSummary, networkPlot, consensusScores, consensusHeatmap, runGSAhyper, GSAheatmap, writeFilesForKiwi, exploreGSAres, networkPlot2 ) S3method(print, ArrayData) S3method(print, GSC) S3method(print, GSAres) import( BiocGenerics, shiny ) importFrom(Biobase, exprs, "exprs<-", featureNames, sampleNames) importFrom(gplots, heatmap.2, venn) importFrom(marray, maColorBar) importFrom(relations, relation_class_ids, relation_consensus) importFrom(grDevices, colorRampPalette, dev.new, dev.off, pdf, rainbow, col2rgb, rgb) importFrom(graphics, abline, barplot, layout, legend, lines, mtext, par, plot, plot.new, points, text, title, axis, hist, rect) importFrom(stats, fisher.test, median, model.matrix, p.adjust, pchisq, pnorm, prcomp, qnorm, rnorm, wilcox.test, dist, setNames) importFrom(utils, capture.output, read.delim, write.table, installed.packages, stack, unstack, write.csv) importFrom(igraph, graph.adjacency, ecount, vcount, ends, layout_with_fr, layout_with_lgl, layout_with_kk, layout_with_graphopt, layout_in_circle, layout_nicely,layout_as_star,layout_with_sugiyama, layout_on_grid, layout_as_tree, layout_on_sphere, layout_randomly, layout_with_dh, layout_with_gem, layout_with_mds) importFrom(fgsea, fgsea) importFrom(DT, selectRows, dataTableProxy) importFrom(htmlwidgets, JS) importFrom(shinyjs, useShinyjs, hidden, show, hide, showElement) importFrom(shinydashboard, dashboardPage, dashboardHeader, dashboardSidebar, dashboardBody, box, tabBox) importFrom(visNetwork, visNetwork, renderVisNetwork, visNetworkOutput, toVisNetworkData, visNodes, visLayout, visPhysics, visIgraphLayout, visExport, "%>%") importFrom(scales, rescale) importFrom(methods, is)