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 |