Package index • RGenEDA

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

Reference