aggregateRankPlot       Create an aggregate rank plot from a summary
                        object
allBenchmarkPlots       Plot the complete list of benchmark summaries
allBenchmarkResults     Generate all benchmark results with some
                        precomputed arguments. This function generates
                        all benchmark results by using precomputed
                        values for 'normSilDF', 'dimMat' and 'maxDist'.
benchmarkPlots          Plot a list of summary data frames
corrPlots               Create correlation plots for method results
corrSummary             Calculate correlation matrix for method results
efficiencyBenchmark     Extract running times and peak memory usage for
                        gene set analysis methods
geneSetRankPlots        Create gene set rank plots for the method
                        results
mdsPlots                Create MDS plots for method results
memoryPlot              Plot a data frame consisting of gene set
                        analysis method peak memory usage This function
                        plots data frame consisting of method peak
                        memory usages with methods as rows, gene sets
                        and the gene set average as columns.
metricRankPlots         Create metric rank plots for the method results
predJaccardPlots        Create Jaccard tile plots for method binary
                        predictions
ratioPlot               Create a ratio rank plot for the method results
runAddModuleScore       Run AddModuleScore
runAUCell               Run AUCell
runBenchmark            Generate all benchmark results This function
                        performs the entire 'GSABenchmark' pipeline.
runBenchmarkShuffle     Generate all benchmark results for shuffled
                        gene sets This function generates all benchmark
                        results for shuffled gene sets.
runGSAMethods           Run gene set analysis methods
runGSVA                 Run GSVA
runJASMINE              Run JASMINE
runMDT                  Run MDT using decoupleR
runMethodShuffle        Run gene set analysis method on shuffled gene
                        sets
runMLM                  Run MLM using decoupleR
runORA                  Run ORA using decoupleR
runPagoda2              Run pagoda2
runPLAGE                Run PLAGE
runSingscore            Run Singscore
runSiPSiC               Run SiPSiC
runssGSEA               Run ssGSEA
runUCell                Run UCell
runUDT                  Run UDT using decoupleR
runVAM                  Run VAM
runZscore               Run Zscore
scorePlot               Plot a data frame consisting of gene set
                        analysis method scores This function plots a
                        data frame consisting of method scores with
                        methods as rows, gene sets and the gene set
                        average as columns.
supportedMethods        Show supported methods
timePlot                Plot a data frame consisting of gene set
                        analysis method running times This function
                        plots data frame consisting of method running
                        times with methods as rows, gene sets and the
                        gene set average as columns.
