Companion package to epiregulon with additional plotting, differential and graph functions

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Documentation for package ‘epiregulon.extra’ version 1.2.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

addCentrality	Creating graphs and related operations
buildDiffGraph	Creating graphs and related operations
buildGraph	Creating graphs and related operations
calculateJaccardSimilarity	Calculate Jaccard Similarity between regulons of all transcription factors
enrichPlot	Plot results of regulonEnrich
findDifferentialActivity	Test for differential TF activity between pairs of single cell clusters/groups
findPartners	Find interaction partners of a transcription factor of interest
getSigGenes	Compile and summarize the output from findDifferentialActivity function
normalizeCentrality	Creating graphs and related operations
permuteGraph	Calculate similarity score from permuted graphs to estimate background similarity
plotActivityDim	Plot cell-level reduced dimension results stored in a SingleCellExperiment object, colored by activities for a list of TFs
plotActivityViolin	Generate violin plots of inferred activities for a list of TFs grouped by cluster/group labels
plotBubble	Generate bubble plots of relative activities across cluster/group labels for a list of TFs
plotDiffNetwork	Plot graph according to grouping factor
plotEpiregulonNetwork	Plot a graph build based on 'getRegulon' output
plotGseaNetwork	Plot networks graph of significant genesets from regulonEnrich results
plotHeatmapActivity	Plot transcription factor activity
plotHeatmapRegulon	Plot targets genes of transcription factors in regulons
rankTfs	Creating graphs and related operations
regulon	regulon created using 'epiregulon' package from reprogram-seq data
regulonEnrich	Perform geneset enrichment of user-defined regulons