DEGAll                  Output of 'gdcDEAnalysis' for downstream
                        analysis
GDCRNATools-package     This is an easy-to-use package for downloading,
                        organizing, and integrative analyzing RNA
                        expression data in GDC with an emphasis on
                        deciphering the lncRNA-mRNA related ceRNA
                        regulatory network in cancer.
enrichOutput            Output of 'gdcEnrichAnalysis' for visualization
gdcBarPlot              Bar plot of differentially expressed
                        genes/miRNAs
gdcCEAnalysis           Competing endogenous RNAs (ceRNAs) analysis
gdcClinicalDownload     Download clinical data in GDC
gdcClinicalMerge        Merge clinical data
gdcCorPlot              Correlation plot of two genes/miRNAs
gdcDEAnalysis           Differential gene expression analysis
gdcDEReport             Report differentially expressed genes/miRNAs
gdcEnrichAnalysis       Functional enrichment analysis
gdcEnrichPlot           Plots for enrichment analysis
gdcExportNetwork        Export network for Cytoscape
gdcFilterDuplicate      Filter out duplicated samples
gdcFilterSampleType     Filter out other type of samples
gdcHeatmap              Heatmap of differentially expressed
                        genes/miRNAs
gdcKMPlot               Kaplan Meier plot
gdcMatchSamples         Match samples in metadata and expression matrix
gdcParseMetadata        Parse metadata
gdcRNADownload          Download RNA data in GDC
gdcRNAMerge             Merge RNA/miRNAs raw counts data
gdcSurvivalAnalysis     Univariate survival analysis of multiple genes
gdcVolcanoPlot          Volcano plot of differentially expressed
                        genes/miRNAs
gdcVoomNormalization    TMM normalization and voom transformation
lncTarget               miRNA-lncRNA interactions
mirCounts               miRNA counts data of TCGA-CHOL
pcTarget                miRNA-mRNA interactions
rnaCounts               RNAseq counts data of TCGA-CHOL
shinyCorPlot            Shiny correlation plot
shinyKMPlot             Shiny Kaplan Meier (KM) plot
shinyPathview           Shiny pathview
