Package: RGenEDA 0.99.0

Michael Martinez

RGenEDA: Genomic Exploratory Data Analysis

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. See <https://github.com/mikemartinez99/RGenEDA>.

Authors:Michael Martinez [aut, cre]

RGenEDA_0.99.0.tar.gz
RGenEDA_0.99.0.zip(r-4.7-any)RGenEDA_0.99.0.zip(r-4.6-any)RGenEDA_0.99.0.zip(r-4.5-any)
RGenEDA_0.99.0.tgz(r-4.6-any)RGenEDA_0.99.0.tgz(r-4.5-any)
RGenEDA_0.99.0.tar.gz(r-4.7-any)RGenEDA_0.99.0.tar.gz(r-4.6-any)
RGenEDA_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RGenEDA/json (API)

# Install 'RGenEDA' in R:

install.packages('RGenEDA', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mikemartinez99/rgeneda/issues

Pkgdown/docs site:https://mikemartinez99.github.io

Datasets:

Snail1KO - Snail1KO dataset

On CRAN:

software rnaseq geneexpression transcriptomics sequencing differentialexpression principalcomponent qualitycontrol visualization

3.69 score 11 scripts 30 exports 55 dependencies

Last updated from:ad98b0ce95. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	205
linux-devel	OK	358
source / vignettes	OK	633
linux-release	OK	278
macos-release	OK	262
macos-oldrel	OK	251
windows-devel	OK	625
windows-release	OK	411
windows-oldrel	OK	608
wasm-release	OK	145

Exports:as.geneda DEDashboard DEGs DimReduction extractEigen ExtractPCA FilterDEGs FindHVDEGs FindVariableFeatures GenEDA generatePCs GenSave getCounts getMetadata getNormalized HVGs PlotCountDist PlotDistances PlotEigenCorr PlotEigenHeatmap PlotHVGVariance PlotMA PlotOrdCorr PlotPCA PlotPValHist PlotScree PlotVolcano RunPCA SetDEGs SummarizeDEGs

Dependencies:abind Biobase BiocGenerics cli cluster cpp11 DelayedArray dplyr farver generics GenomicRanges ggplot2 ggrepel glue gtable IRanges isoband labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv nlme patchwork permute pheatmap pillar pkgconfig purrr R6 RColorBrewer Rcpp rlang S4Arrays S4Vectors S7 scales Seqinfo SparseArray stringi stringr SummarizedExperiment tibble tidyr tidyselect utf8 vctrs vegan viridisLite withr XVector

RGenEDA Tutorial

Rendered fromSnail1_Vignette.Rmdusingknitr::rmarkdown

Last update: 2026-10-30
Started: 2025-11-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert a SummarizedExperiment to a geneda object	as.geneda as.geneda,SummarizedExperiment-method
DEDashboard	DEDashboard
Access DEGs container	DEGs
Access dimensional reduction results list	DimReduction
extractEigen	extractEigen
Extract PCA Loadings and Metadata	ExtractPCA
Filter DEGs by padj and absolute log2FoldChange	FilterDEGs
Find DEGs Overlapping With HVGs	FindHVDEGs
Find and store highly variable genes (HVGs)	FindVariableFeatures
Construct a geneda object	GenEDA
geneda S4 class	geneda-class
generatePCs	generatePCs
Save a pheatmap Objects generated from RGenEDA to File	GenSave
Access counts matrix (avoid name clash with DESeq2::counts)	getCounts
Access metadata (avoid name clash with S4 generics)	getMetadata
Access normalized matrix (avoid name clash with generics)	getNormalized
Access HVG IDs	HVGs
PlotCountDist	PlotCountDist
Plot a Euclidean Distance Heatmap	PlotDistances
Plot Eigen-Correlation With Metadata Heatmap	PlotEigenCorr
PlotEigenHeatmap	PlotEigenHeatmap
PlotHVGVariance	PlotHVGVariance
PlotMA	PlotMA
Plot Ordination Correlations With Metadata Heatmap	PlotOrdCorr
Plot PCA results from a GenEDA object	PlotPCA
PlotPValHist	PlotPValHist
PlotScree	PlotScree
PlotVolcano	PlotVolcano
Run PCA and store in 'DimReduction'	RunPCA
Set unfiltered DEGs on the object	SetDEGs
Show method for geneda	show,geneda-method
Snail1KO dataset	Snail1KO
Summarize DEGs Across Selected Assays	SummarizeDEGs