RGenEDA

Clean, unified, streamlined, and reproducible frameworks for genomic exploratory data analyses

Warning

RGenEDA has updated to v2.0.0 which introduced some breaking changes. Please ensure you are using the most up-to-date version

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Installation

Install the latest version from Github

install.packages("devtools") # if not already instaled

library(devtools)
devtools::install_github("mikemartinez99/RGenEDA")

library(RGenEDA)

Usage

For a full demo, see Snail1 KO Dataset Demo

For some background on why EDA is important, see Compute and Conquer: The Basics of EDA

Change-log

April 2025: "The poor-man's EDA"

• Implemented core, standalone functions
  
  • Variance calculation, PCA calculation, and Eucliden distances, and Eigenvector correlations
    

October 16th, 2025: "The GenEDA Object Update

• Introduced S4 GenEDA object for streamlined data handling
  
• Added methods for HVG calculation and PCA storage within S4 slots
  
• Added visualization functions
  
  • PCA plots
    
  • Variance plots for HVGs
    
  • Eigenvector (gene-loading) plots
    
• Revamped eigencorrelation plots to only use top number of HVGs identified in HVG selection/PCA
  
• Enhanced plot output flexibility (return ggplot2, pheatmap, or ComplexHeatmap objects for full customization
  
• Added unit tests
  
• Added Pasilla dataset vignette
  

November 3rd, 2025

• Rely soley on Pheatmap for all heatmap visualizations
  
• Fixed top-gene-loading bug for selected PCs in PlotEigenHeatmap function
  
• Added optional DEGs slot to GenEDA object to interface with DESeq2
  
• Added MA plot functionality
  

November 10th, 2025

• Fixed example blocks in roxygen headers
  
• Addressed all R cmd build errors, warnings, and notes
  

November 15th, 2025: "The DEG update"

• Added assay argument to SetDEGs function
  
• Added assay and saveAssay argument to FilterDEGs function to specify which assay to filter and what to save filtered assay as
  
• Added assay argument to PlotMA to specify which DEG slot to plot
  
• Added PlotVolcano function for direct volcano plotting functionality
  
• Added FindHVDEGs to intersect DEGs with HVGs calculated during EDA functions
  
• Added GenSave function to save save pheatmap objects in a manner similar to ggplpot2::ggsave()
  
• Renamed eigencorr, ordcorr, and distanceHeatmap functions to PlotEigenCorr, PlotOrdCorr, and PlotDistances respectively to match other plotting function name conventions
  
• Replaced Pasilla dataset demo with Snail1 KO dataset from Matsuri et al., 2018
  

January 21st, 2026

• Added in PlotScree function
  
• Updated PCA utilities to dynamically generate PCs up until PC10
• Renamed the DimReduction$Loadings slot to DimReduction$Scores to more accurately reflect the information contained in this slot
• Added Scree Plot to vignette
  

February 13th, 2026

• Fixed bug in RunPCA where PCs beyond 10 are named as NA
  
• Fixed bug in PlotScree where PCs beyond 10 are shown as NA
  

Citation

If you use RGenEDA in your work, please cite: dx.doi.org/10.17504/protocols.io.bp2l6z6rdgqe/v1

📬 Contact

Mike Martinez M.S. - Dartmouth Genomic Data Science Core

f007qps@dartmouth.edu