ExamplePathways         Example pathway database
ExampleResults          Example results from runLimmaAnalysis
NanoTube                NanoTube
deVolcano               Draw volcano plot of differential expression
                        results
fgseaPostprocessing     Postprocessing for GSEA analyses
fgseaPostprocessingXLSX
                        Postprocessing for GSEA analyses for Excel
fgseaToLEdge            Generate leading edge matrix from fgsea
                        results.
gm_mean                 Calculate the geometric mean
groupFGSEA              Cluster gene set analysis results
groupedGSEAtoStackedReport
                        Build a report from gene set enrichment
                        results.
limmaToFGSEA            Run gene set enrichment analysis using DE
                        results.
makeDiffExprFile        Make differential expression results file.
makeFGSEAmasterTable    Make master table of all GSEA results
makeNanoStringSetFromEset
                        Convert NanoString ExpressionSet to
                        NanoStringSet
nanostringPCA           Plot PCA
negativeQC              Calculate negative control statistics
normalize_housekeeping
                        Housekeeping gene normalization
normalize_pos_controls
                        Positive control gene normalization
nsdiffToFGSEA           Run gene set enrichment analysis using DE
                        results.
positiveQC              Calculate positive control statistics
processNanostringData   Process NanoString nCounter gene expression
                        data.
read_cpdb_sourceDBs     Identify source databases from a .tab file
read_cpdb_tab           Read .tab file.
read_merge_rcc          Merge multiple .rcc files
read_rcc                Read .rcc file
read_sampleData         Read in a sample data table.
remove_background       Assess background expression
runLimmaAnalysis        Conduct differential expression analysis
untar_dirs              Untar
unzip_dirs              Unzip
