Nov 25, 2025

Public workspaceRGenEDA (R package)

DOI
https://dx.doi.org/10.17504/protocols.io.bp2l6z6rdgqe/v1
RGenEDA (R package)
  • Michael Martinez1
  • 1Dartmouth College
  • RGenEDA
Michael J Martinez
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DOI: https://dx.doi.org/10.17504/protocols.io.bp2l6z6rdgqe/v1
External link: https://github.com/mikemartinez99/RGenEDA
Protocol Citation: Michael Martinez 2025. RGenEDA (R package). protocols.io https://dx.doi.org/10.17504/protocols.io.bp2l6z6rdgqe/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: November 14, 2025
Last Modified: November 25, 2025
Protocol Integer ID: 232424
Keywords: Genomics, Exploratory Data Analysis, PCA, RNASeq, metagenomics, MGX, eigenvectors, eigencorrelation, Euclidean distances, RNA, DNA, multi-omics, multi-omics analysis, automated plotting, genomic exploratory data analysis, rgeneda, performing genomic exploratory data analysis, eda, reproducible framework, data, analysis
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Abstract
RGenEDA is an R package that provides a unified and reproducible framework for performing genomic exploratory data analysis (EDA). Highly repetitive functions and analyses have been collated into an easy-to-use S4 object that produces quick results and customizable visualizations to assess variation in your data.
Guidelines
For a tutorial on the base functions of RGenEDA, see vignette at https://mikemartinez99.github.io/RGenEDA/articles/Snail1_Vignette.html
Materials
- A computer capable of running R (>= 4.1.0) and/or RStudio.

- Multi-omics data ready to be analyzed
Troubleshooting
Safety warnings
RGenEDA relies on the following R package dependencies:

R (> 4.1.0)
pheatmap
RColorBrewer
dplyr
ggplot2
ggrepel
grid
scales
tidyr
vegan
stats
Before start
Ensure you have the most up-to-date version of RGenEDA installed, as the package is regularly updated.
Installation

Command
Install RGenEDA from devtools
install.packages(devtools) # if not already instaled

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

library(RGenEDA)

Running RGenEDA (Vignette)
For a detailed vignette, please visit the Github here: https://github.com/mikemartinez99/RGenEDA or documentation / vignettes here: https://mikemartinez99.github.io/RGenEDA/articles/Snail1_Vignette.html