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

as.geneda(): Convert a SummarizedExperiment to a geneda object

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