Tools for benchmarking single-cell gene set analysis methods

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Documentation for package ‘GSABenchmark’ version 0.99.8

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

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.