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
  

October 29th, 2026

• Fixed cosmetics of printing statements
  
• Minor bug fixes in PCA functions and accessors
  

Bioconductor submission

• Renumbered to 0.99.0 following Bioconductor versioning conventions (continues from 2.1.0)
  
• Added biocViews, URL, and BugReports to DESCRIPTION
  
• Added as.geneda() to create GenEDA objects directly from SummarizedExperiment, DESeqDataSet, and DESeqTransform objects
  
• Added runnable examples for all exported functions using the bundled Snail1KO data
  
• Restyled code to Bioconductor style (4-space indents, 80-character lines)
  

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