import( 'locfit' ) importFrom( 'DESeq', 'newCountDataSet', 'estimateSizeFactors', 'estimateDispersions', 'nbinomTest', 'getVarianceStabilizedData') importFrom( 'DESeq2', 'DESeqDataSetFromMatrix', 'estimateSizeFactors', 'estimateDispersions', 'nbinomWaldTest', 'results') importFrom( 'samr', 'SAMseq' ) importFrom( 'limma', 'voom', 'lmFit', 'eBayes' ) importFrom( 'EBSeq', 'MedianNorm', 'EBTest', 'GetPPMat') importFrom( 'NBPSeq', 'nbp.test') importFrom( 'edgeR', 'DGEList', 'exactTest', 'calcNormFactors', 'estimateCommonDisp', 'estimateTagwiseDisp') importFrom( 'graph', 'ugraph') importFrom( 'RBGL', 'kCliques') importFrom( 'igraph', 'igraph.to.graphNEL', 'graph_from_edgelist', 'as_data_frame', 'closeness', 'hub_score', 'decompose', 'cluster_walktrap', 'cluster_edge_betweenness', 'cluster_fast_greedy', 'cluster_leading_eigen', 'cluster_infomap', 'cluster_louvain', 'cliques', 'max_cliques', 'coreness', 'components', 'as.undirected', 'betweenness', 'eccentricity', 'articulation_points', 'page_rank', 'degree', 'dfs', 'ego', 'get.edgelist', 'get.adjacency', 'graph.adjacency', 'graph.adjlist', 'V', 'E', 'all_simple_paths', 'graph.data.frame', 'simplify', 'V<-', 'E<-', 'layout.davidson.harel', 'write.graph') importFrom( 'Matrix', 'triu') importFrom( 'circlize', 'circos.par', 'chordDiagram', 'get.all.sector.index', 'get.cell.meta.data', 'circos.text', 'circos.clear') importFrom( 'grDevices', 'pdf', 'png', 'svg', 'rainbow', 'dev.off', 'colorRampPalette', 'dev.copy2pdf') importFrom( 'graphics', 'par', 'barplot', 'text', 'plot') importFrom( 'stats', 'deviance', 'glm', 'hatvalues', 'pchisq', 'pf', 'poisson', 'qchisq', 'qf', 'residuals', 'p.adjust', 'phyper', 'model.matrix', 'cor', 'predict') importFrom( 'pheatmap', 'pheatmap') importFrom( 'utils', 'browseURL', 'head', 'write.table', 'read.table', 'capture.output') importFrom( 'ggplot2', 'qplot', 'theme_classic', 'geom_point', 'scale_colour_gradientn', 'labs', 'cut_number', 'theme', 'element_text') importFrom( 'jsonlite', 'toJSON') importFrom( 'tools', 'file_ext') importFrom( 'methods', 'representation', 'setClass', 'setGeneric', 'setMethod', 'signature', 'new') export( 'DEsubs', 'geneVisualization', 'organismVisualization', 'subpathwayToGraph', 'subpathwayVisualization', 'subpathwayTypes' )