| analysis.averageCorrelation | Predefined enrichment analyses | 
| analysis.averageTStatistic | Predefined enrichment analyses | 
| analysis.customOverrepresentation | Predefined enrichment analyses | 
| analysis.globalAncova | Predefined enrichment analyses | 
| analysis.globalTest | Predefined enrichment analyses | 
| analysis.gsea | Predefined enrichment analyses | 
| analysis.overrepresentation | Predefined enrichment analyses | 
| countdata | Example data | 
| createSummaryTable | Create an overview table for an analysis | 
| evaluateGeneSetUncertainty | Quantify gene set uncertainty | 
| filterGeneSets | Filtering of gene sets | 
| geneSetAnalysis | Main interface for enrichment analyses. | 
| GiANT | Enrichment analysis | 
| global | Global analyses | 
| global.ancova | Global analyses | 
| global.overrepresentation | Global analyses | 
| global.test | Global analyses | 
| gls | Gene-level statistics | 
| gls.cor | Gene-level statistics | 
| gls.foldChange | Gene-level statistics | 
| gls.moderateTStatistic | Gene-level statistics | 
| gls.nBinomTest | Gene-level statistics | 
| gls.regression | Gene-level statistics | 
| gls.tStatistic | Gene-level statistics | 
| gsAnalysis | Gene set analysis. | 
| gss | Gene set statistics | 
| gss.enrichmentScore | Gene set statistics | 
| gss.fisherExactTest | Gene set statistics | 
| gss.gsz | Gene set statistics | 
| gss.maxmean | Gene set statistics | 
| gss.mean | Gene set statistics | 
| gss.median | Gene set statistics | 
| gss.sum | Gene set statistics | 
| gss.wilcoxonRankTest | Gene set statistics | 
| hist.gsaResult | Null distribution histogram and statistic of the input set for enrichment analyses. | 
| labels | Example data to label samples in countdata (rows) in two classes 0 and 1 | 
| mergeProbesForGenes | Merge multiple probes for one gene | 
| parseGmt | Venn Euler Diagramm | 
| pathways | Example data for pathways to to gene set enrichtment analyses | 
| plot.uncertaintyResult | Plots the results of an uncertainty analysis. | 
| plotOverrepresentation | Plot overlap of gene sets and core set | 
| predefinedAnalyses | Predefined enrichment analyses | 
| preprocessGeneSets | Eliminate unknown genes from gene sets | 
| preprocessGs | Eliminate unknown genes from gene sets | 
| significance | Significance assessment | 
| significance.permutation | Significance assessment | 
| significance.restandardization | Significance assessment | 
| significance.sampling | Significance assessment | 
| summary.gsaResult | Summarize gene set analysis results | 
| transformation | Transformations | 
| transformation.abs | Transformations | 
| transformation.adjust | Transformations | 
| transformation.adjustAndBinarize | Transformations | 
| transformation.binarize | Transformations | 
| transformation.localFdr | Transformations | 
| transformation.rank | Transformations | 
| transformation.square | Transformations |