Binned Motif Enrichment Analysis and Visualization

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Documentation for package ‘monaLisa’ version 1.13.3

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

Help Pages

annoSeqlogo	Sequence logo annotation
bin	Bin elements of 'x'.
calcBinnedKmerEnr	Calculate k-mer enrichment in bins of sequences.
calcBinnedMotifEnrHomer	Prepare and run HOMER motif enrichment analysis.
calcBinnedMotifEnrR	Binned Motif Enrichment Analysis with 'monaLisa'
dumpJaspar	Dump Jaspar motifs into a HOMER motif file.
findHomer	Find HOMER script file.
findMotifHits	Find motif matches in sequences.
findMotifHits-method	Find motif matches in sequences.
getColsByBin	Get colors by bin.
getKmerFreq	Calculate observed and expected k-mer frequencies
getSetZeroBin	Get and set the zero bin manually
getZeroBin	Get and set the zero bin manually
homerToPFMatrixList	Read a HOMER motif file and create a PFMatrixList
motifKmerSimilarity	Calculate similarities between motifs and k-mers.
motifSimilarity	Calculate similarities between pairs of motifs.
parseHomerOutput	Load output from HOMER findMotifsGenome.pl into R
plotBinDensity	Density plot of binned elements.
plotBinDiagnostics	Plot diagnostics of binned sequences
plotBinHist	Histogram of binned elements.
plotBinScatter	Scatter plot (xy-plot) of binned elements.
plotMotifHeatmaps	Heatmap of motif enrichments.
plotSelectionProb	Plot selection probabilities of predictors
plotStabilityPaths	Plot Stability Paths
prepareHomer	Prepare input files for HOMER motif enrichment analysis.
randLassoStabSel	Randomized Lasso Stability Selection
sampleRandomRegions	Sample random regions of fixed length.
seqLogoGrob	Create a simple sequence logo grob.
setZeroBin	Get and set the zero bin manually