monaLisa-package	monaLisa-package
.calcKmerEnrichment	dot-calcKmerEnrichment
.calcMotifEnrichment	dot-calcMotifEnrichment
.calculateGCweight	dot-calculateGCweight
.checkDfValidity	dot-checkDfValidity
.checkIfSeqsAreEqualLength	dot-checkIfSeqsAreEqualLength
.cons2matrix	dot-cons2matrix
.defineBackground	dot-defineBackground
.filterSeqs	dot-filterSeqs
.glmnetRandomizedLasso	dot-glmnetRandomizedLasso
.iterativeNormForKmers	dot-iterativeNormForKmers
.normForKmers	dot-normForKmers
annoSeqlogo	annoSeqlogo
bin	bin
calcBinnedKmerEnr	calcBinnedKmerEnr
calcBinnedMotifEnrHomer	calcBinnedMotifEnrHomer
calcBinnedMotifEnrR	calcBinnedMotifEnrR
dumpJaspar	dumpJaspar
findHomer	findHomer
findMotifHits	findMotifHits-methods
findMotifHits,character,character-method	findMotifHits-methods
findMotifHits,character,DNAString-method	findMotifHits-methods
findMotifHits,character,DNAStringSet-method	findMotifHits-methods
findMotifHits,PWMatrix,character-method	findMotifHits-methods
findMotifHits,PWMatrix,DNAString-method	findMotifHits-methods
findMotifHits,PWMatrix,DNAStringSet-method	findMotifHits-methods
findMotifHits,PWMatrix,GRanges-method	findMotifHits-methods
findMotifHits,PWMatrixList,character-method	findMotifHits-methods
findMotifHits,PWMatrixList,DNAString-method	findMotifHits-methods
findMotifHits,PWMatrixList,DNAStringSet-method	findMotifHits-methods
findMotifHits,PWMatrixList,GRanges-method	findMotifHits-methods
getColsByBin	getColsByBin
getKmerFreq	getKmerFreq
getSetZeroBin	getSetZeroBin
getZeroBin	getSetZeroBin
homerToPFMatrixList	homerToPFMatrixList
monaLisa	monaLisa-package
motifKmerSimilarity	motifKmerSimilarity
motifSimilarity	motifSimilarity
parseHomerOutput	parseHomerOutput
plotBinDensity	plotBinDensity
plotBinDiagnostics	plotBinDiagnostics
plotBinHist	plotBinHist
plotBinScatter	plotBinScatter
plotMotifHeatmaps	plotMotifHeatmaps
plotSelectionProb	plotSelectionProb
plotStabilityPaths	plotStabilityPaths
prepareHomer	prepareHomer
randLassoStabSel	randLassoStabSel
sampleRandomRegions	sampleRandomRegions
seqLogoGrob	seqLogoGrob
setZeroBin	getSetZeroBin
