Package: monaLisa 1.13.2

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]

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monaLisa.pdf |monaLisa.html✨
monaLisa/json (API)
NEWS

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

Peer review:

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

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

On BioConductor:monaLisa-1.13.1(bioc 3.21)monaLisa-1.12.0(bioc 3.20)

motifannotationvisualizationfeatureextractionepigenetics

8.00 score 39 stars 53 scripts 304 downloads 27 exports 134 dependencies

Last updated 2 days agofrom:2647c7fab0. Checks:1 OK, 6 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 21 2025
R-4.5-winERRORJan 21 2025
R-4.5-linuxERRORJan 21 2025
R-4.4-winERRORJan 21 2025
R-4.4-macERRORJan 21 2025
R-4.3-winERRORJan 21 2025
R-4.3-macERRORJan 21 2025

Exports:annoSeqlogobincalcBinnedKmerEnrcalcBinnedMotifEnrHomercalcBinnedMotifEnrRdumpJasparfindHomerfindMotifHitsgetColsByBingetKmerFreqgetZeroBinhomerToPFMatrixListmotifKmerSimilaritymotifSimilarityparseHomerOutputplotBinDensityplotBinDiagnosticsplotBinHistplotBinScatterplotMotifHeatmapsplotSelectionProbplotStabilityPathsprepareHomerrandLassoStabSelsampleRandomRegionsseqLogoGrobsetZeroBin

Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcaToolscirclizeclicliprclueclusterCNErcodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIDelayedArraydigestDirichletMultinomialdoParallelfansifarverfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesGetoptLongggplot2glmnetGlobalOptionsglueGO.dbgtablegtoolshmshttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngpoweRlawpracmaprettyunitsprogresspwalignR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenRCurlreadrreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesseqLogoshapesmsnowSparseArraystabsstringistringrSummarizedExperimentsurvivalsysTFBSToolsTFMPvaluetibbletidyselecttzdbUCSC.utilsutf8vctrsvioplotviridisLitevroomwithrXMLxtableXVectoryamlzoo

monaLisa - MOtif aNAlysis with Lisa

Dania Machlab, Lukas Burger, Charlotte Soneson, Michael Stadler

Rendered frommonaLisa.Rmdusingknitr::rmarkdownon Jan 21 2025.

Last update: 2022-01-25
Started: 2019-09-27

Regression Based Approach for Motif Selection

Dania Machlab, Lukas Burger, Charlotte Soneson, Michael Stadler

Rendered fromselecting_motifs_with_randLassoStabSel.Rmdusingknitr::rmarkdownon Jan 21 2025.

Last update: 2022-01-25
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