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.
getColsByBin            Get colors by bin.
getKmerFreq             Calculate observed and expected k-mer
                        frequencies
getSetZeroBin           Get and set the zero bin manually
homerToPFMatrixList     Read a HOMER motif file and create a
                        PFMatrixList
monaLisa-package        monaLisa - MOtif aNAlysis with Lisa.
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.
