Package: monaLisa 1.19.0

Michael Stadler

monaLisa: Binned Motif Enrichment Analysis and Visualization

Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of the obtained results are also provided.

Authors:Dania Machlab [aut], Lukas Burger [aut], Charlotte Soneson [aut], Dany Mukesha [ctb], Michael Stadler [aut, cre]

monaLisa_1.19.0.tar.gz
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monaLisa_1.19.0.tgz(r-4.6-any)monaLisa_1.19.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
monaLisa/json (API)

# Install 'monaLisa' in R:
install.packages('monaLisa', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fmicompbio/monalisa/issues

Pkgdown/docs site:https://fmicompbio.github.io

On BioConductor:monaLisa-1.19.0(bioc 3.24)monaLisa-1.18.0(bioc 3.23)

motifannotationvisualizationfeatureextractionepigenetics

8.23 score 47 stars 87 scripts 612 downloads 27 exports 109 dependencies

Last updated from:dfdf4c3ef3. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE290
linux-devel-x86_64OK555
source / vignettesOK533
linux-release-x86_64OK551
macos-release-arm64OK472
macos-oldrel-arm64OK484
windows-develOK513
windows-releaseOK496
windows-oldrelOK463
wasm-releaseOK248

Exports:annoSeqlogobincalcBinnedKmerEnrcalcBinnedMotifEnrHomercalcBinnedMotifEnrRdumpJasparfindHomerfindMotifHitsgetColsByBingetKmerFreqgetZeroBinhomerToPFMatrixListmotifKmerSimilaritymotifSimilarityparseHomerOutputplotBinDensityplotBinDiagnosticsplotBinHistplotBinScatterplotMotifHeatmapsplotSelectionProbplotStabilityPathsprepareHomerrandLassoStabSelsampleRandomRegionsseqLogoGrobsetZeroBin

Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcaToolscigarillocirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIDelayedArraydigestDirichletMultinomialdoParalleldplyrfarverfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesGetoptLongggplot2glmnetGlobalOptionsgluegtablegtoolshttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrpwalignR6RColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfoseqLogoshapesnowSparseArraystabsstringistringrSummarizedExperimentsurvivalsysTFBSToolsTFMPvaluetibbletidyrtidyselectutf8vctrsviridisLitewithrXMLXVectoryaml

monaLisa - MOtif aNAlysis with Lisa
Introduction | Installation | Quick example: Identify enriched motifs in bins | Binned motif enrichment analysis with multiple sets of sequences (more than two): Finding TFs enriched in differentially methylated regions | Load packages | Genomic regions or sequences of interest | Bin genomic regions | Prepare motif enrichment analysis | Run motif enrichment analysis | Convert between motif text file for Homer and motif objects in R | Motif enrichment analysis with only one or two sets of sequences | Binary motif enrichment analysis: comparing two sets of sequences | Single set motif enrichment analysis: comparing a set of sequences to a suitable background | Binned k-mer enrichment analysis | Use r Biocpkg("monaLisa") to annotate genomic regions with predicted motifs | Session info and logo | References
Rendered frommonaLisa.Rmdusingknitr::rmarkdown

Last update: 2025-03-24
Started: 2019-09-27

Regression Based Approach for Motif Selection
Introduction | Motif selection with Randomized Lasso Stability Selection | Load packages | Load dataset | Get TFBS per motif and peak | A note on collinearity | Identify important TFs | Session info and logo | References
Rendered fromselecting_motifs_with_randLassoStabSel.Rmdusingknitr::rmarkdown

Last update: 2025-03-24
Started: 2021-09-10

Readme and manuals

Help Manual

Help pageTopics
Sequence logo annotationannoSeqlogo
Bin elements of 'x'.bin
Calculate k-mer enrichment in bins of sequences.calcBinnedKmerEnr
Prepare and run HOMER motif enrichment analysis.calcBinnedMotifEnrHomer
Binned Motif Enrichment Analysis with 'monaLisa'calcBinnedMotifEnrR
Dump Jaspar motifs into a HOMER motif file.dumpJaspar
Find HOMER script file.findHomer
Find motif matches in sequences.findMotifHits findMotifHits,character,character-method findMotifHits,character,DNAString-method findMotifHits,character,DNAStringSet-method findMotifHits,PWMatrix,character-method findMotifHits,PWMatrix,DNAString-method findMotifHits,PWMatrix,DNAStringSet-method findMotifHits,PWMatrix,GRanges-method findMotifHits,PWMatrixList,character-method findMotifHits,PWMatrixList,DNAString-method findMotifHits,PWMatrixList,DNAStringSet-method findMotifHits,PWMatrixList,GRanges-method
Get colors by bin.getColsByBin
Calculate observed and expected k-mer frequenciesgetKmerFreq
Get and set the zero bin manuallygetSetZeroBin getZeroBin setZeroBin
Read a HOMER motif file and create a PFMatrixListhomerToPFMatrixList
Calculate similarities between motifs and k-mers.motifKmerSimilarity
Calculate similarities between pairs of motifs.motifSimilarity
Load output from HOMER findMotifsGenome.pl into RparseHomerOutput
Density plot of binned elements.plotBinDensity
Plot diagnostics of binned sequencesplotBinDiagnostics
Histogram of binned elements.plotBinHist
Scatter plot (xy-plot) of binned elements.plotBinScatter
Heatmap of motif enrichments.plotMotifHeatmaps
Plot selection probabilities of predictorsplotSelectionProb
Plot Stability PathsplotStabilityPaths
Prepare input files for HOMER motif enrichment analysis.prepareHomer
Randomized Lasso Stability SelectionrandLassoStabSel
Sample random regions of fixed length.sampleRandomRegions
Create a simple sequence logo grob.seqLogoGrob