AUC_Scores              Generate Heatmaps for AUC Scores using ggplot2
CalculateScores         Calculate Gene Signature Scores using
                        Score-Based Approaches
CohenD_IndividualGenes
                        Cohen's d Heatmap Function
CorrelationHeatmap      CorrelationHeatmap: Generate correlation
                        heatmaps with optional grouping
ExpressionHeatmap       ExpressionHeatmap: Generate an expression
                        heatmap with customizable sample annotations
                        and separate legend positions
FPR_Simulation          FPR Simulation Plot
IndividualGenes_Violins
                        Generate Violin Plots for Individual Genes
PlotScores              Plot gene signature scores using various
                        methods.
ROC_Scores              Plot ROC Curves for Gene Signature Scores
ROCandAUCplot           ROC and AUC Plot Function
VariableAssociation     Variable Association Analysis
VisualiseIndividualGenes
                        VisualiseIndividualGenes: Wrapper for
                        Visualising Individual Genes in Gene Sets
calculateDE             Calculate Differential Gene Expression
                        Statistics using limma
counts_example          Gene Expression Counts for Marthandan et al.
                        (2016) RNA-Seq Data
geneset_similarity      Plot Signature Similarity via Jaccard Index or
                        Fisher's Odds Ratio
genesets_example        Example Gene Sets for Cellular Senescence
markeR                  markeR: An R Toolkit for Evaluating Gene
                        Signatures as Phenotypic Markers
metadata_example        Metadata for Marthandan et al. (2016) RNA-Seq
                        Study
plotCombinedGSEA        Plot Combined GSEA Results
plotGSEAenrichment      Plot GSEA Enrichment Results
plotNESlollipop         Create a Lollipop Plot for GSEA Results
plotPCA                 Principal Component Analysis (PCA) Plot
plotVolcano             Volcano Plots from Differential Expression
                        Results
runGSEA                 Run Gene Set Enrichment Analysis (GSEA) for
                        Multiple Contrasts
