Package index • markeR

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markeR markeR-package: markeR: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers

Example Data

counts_example: Gene Expression Counts for Marthandan et al. (2016) RNA-Seq Data

metadata_example: Metadata for Marthandan et al. (2016) RNA-Seq Study

Signature Homology

signature_similarity(): Plot Signature Similarity via Jaccard Index

Score-based Analysis

CalculateScores(): Calculate Gene Signature Scores using Score-Based Approaches

PlotScores(): Plot gene signature scores using various methods.

ROC_Scores(): Plot ROC Curves for Gene Signature Scores

AUC_Scores(): Generate Heatmaps for AUC Scores using ggplot2

FPR_Simulation(): FPR Simulation Plot

Enrichment-based Methods

calculateDE(): Calculate Differential Gene Expression Statistics using limma

plotVolcano(): Volcano Plots from Differential Expression Results

runGSEA(): Run Gene Set Enrichment Analysis (GSEA) for Multiple Contrasts

plotGSEAenrichment(): Plot GSEA Enrichment Results

plotNESlollipop(): Create a Lollipop Plot for GSEA Results

plotCombinedGSEA(): Plot Combined GSEA Results

Variable Association

Score_VariableAssociation(): Score Variable Association

GSEA_VariableAssociation(): GSEA Variable Association

Visualization Functions

IndividualGenes_Violins(): Generate Violin Plots for Individual Genes

CorrelationHeatmap(): CorrelationHeatmap: Generate correlation heatmaps with optional grouping

ExpressionHeatmap(): ExpressionHeatmap: Generate an expression heatmap with customizable sample annotations and separate legend positions

ROCandAUCplot(): ROC and AUC Plot Function

CohenD_IndividualGenes(): Cohen's d Heatmap Function

plotPCA(): Principal Component Analysis (PCA) Plot