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