# An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers

## Documentation for package ‘markeR’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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