DOI: 10.18129/B9.bioc.monaLisa  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see monaLisa.

Binned Motif Enrichment Analysis and Visualization

Bioconductor version: 3.16

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.

Author: Dania Machlab [aut] , Lukas Burger [aut], Charlotte Soneson [aut] , Michael Stadler [aut, cre]

Maintainer: Michael Stadler <michael.stadler at>

Citation (from within R, enter citation("monaLisa")):


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HTML R Script monaLisa - MOtif aNAlysis with Lisa
HTML R Script selecting_motifs_with_randLassoStabSel
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biocViews Epigenetics, FeatureExtraction, MotifAnnotation, Software, Visualization
Version 1.4.0
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
License GPL (>= 3)
Depends R (>= 4.1)
Imports methods, stats, utils, grDevices, graphics, BiocGenerics, GenomicRanges, TFBSTools, Biostrings, IRanges, stabs, BSgenome, glmnet, S4Vectors, SummarizedExperiment, BiocParallel, grid, circlize, ComplexHeatmap(>= 2.11.1), XVector, GenomeInfoDb, tools, vioplot
Suggests JASPAR2020, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra
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