An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers

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Documentation for package ‘markeR’ version 0.99.5

• 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