Package: monaLisa 1.11.1

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], 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'))

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

On BioConductor:monaLisa-1.11.1(bioc 3.20)monaLisa-1.10.0(bioc 3.19)

bioconductor-package

27 exports 0.91 score 134 dependencies

Last updated 2 months agofrom:7fcdfe02d0

Exports:annoSeqlogo bin calcBinnedKmerEnr calcBinnedMotifEnrHomer calcBinnedMotifEnrR dumpJaspar findHomer findMotifHits getColsByBin getKmerFreq getZeroBin homerToPFMatrixList motifKmerSimilarity motifSimilarity parseHomerOutput plotBinDensity plotBinDiagnostics plotBinHist plotBinScatter plotMotifHeatmaps plotSelectionProb plotStabilityPaths prepareHomer randLassoStabSel sampleRandomRegions seqLogoGrob setZeroBin

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem caTools circlize cli clipr clue cluster CNEr codetools colorspace ComplexHeatmap cpp11 crayon curl DBI DelayedArray digest DirichletMultinomial doParallel fansi farver fastmap foreach formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges GetoptLong ggplot2 glmnet GlobalOptions glue GO.db gtable gtools hms httr IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png poweRlaw pracma prettyunits progress pwalign R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppEigen RCurl readr reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales seqLogo shape sm snow SparseArray stabs stringi stringr SummarizedExperiment survival sys TFBSTools TFMPvalue tibble tidyselect tzdb UCSC.utils utf8 vctrs vioplot viridisLite vroom withr XML xtable XVector yaml zlibbioc zoo

monaLisa - MOtif aNAlysis with Lisa

Dania Machlab, Lukas Burger, Charlotte Soneson, Michael Stadler

Rendered frommonaLisa.Rmdusingknitr::rmarkdownon Jun 18 2024.

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 Jun 18 2024.

Last update: 2022-01-25
Started: 2021-09-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Sequence logo annotation	annoSeqlogo
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 frequencies	getKmerFreq
Get and set the zero bin manually	getSetZeroBin getZeroBin setZeroBin
Read a HOMER motif file and create a PFMatrixList	homerToPFMatrixList
Calculate similarities between motifs and k-mers.	motifKmerSimilarity
Calculate similarities between pairs of motifs.	motifSimilarity
load output from HOMER findMotifsGenome.pl into R	parseHomerOutput
Density plot of binned elements.	plotBinDensity
Plot diagnostics of binned sequences	plotBinDiagnostics
Histogram of binned elements.	plotBinHist
Scatter plot (xy-plot) of binned elements.	plotBinScatter
Heatmap of motif enrichments.	plotMotifHeatmaps
Plot selection probabilities of predictors	plotSelectionProb
Plot Stability Paths	plotStabilityPaths
Prepare input files for HOMER motif enrichment analysis.	prepareHomer
Randomized Lasso Stability Selection	randLassoStabSel
Sample random regions of fixed length.	sampleRandomRegions
Create a simple sequence logo grob.	seqLogoGrob