| deVolcano | Draw volcano plot of differential expression results | 
| ExamplePathways | Example pathway database | 
| ExampleResults | Example results from runLimmaAnalysis | 
| 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 | 
| groupedGSEAtoStackedReport | Build a report from gene set enrichment results. | 
| groupFGSEA | Cluster gene set analysis 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 | 
| NanoTube | NanoTube | 
| 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 |