# Binned Motif Enrichment Analysis and Visualization

## Documentation for package ‘monaLisa’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

monaLisa-package | monaLisa - MOtif aNAlysis with Lisa.
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
monaLisa | 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.
setZeroBin | Get and set the zero bin manually