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This is the development version of monaLisa; for the stable release version, see monaLisa.

Binned Motif Enrichment Analysis and Visualization

Bioconductor version: Development (3.20)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

monaLisa - MOtif aNAlysis with Lisa HTML R Script
selecting_motifs_with_randLassoStabSel HTML R Script
Reference Manual PDF


biocViews Epigenetics, FeatureExtraction, MotifAnnotation, Software, Visualization
Version 1.11.2
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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, RSQLite
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Suggests JASPAR2020, JASPAR2024, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra
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Follow Installation instructions to use this package in your R session.

Source Package monaLisa_1.11.2.tar.gz
Windows Binary
macOS Binary (x86_64) monaLisa_1.11.2.tgz
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Source Repository git clone
Source Repository (Developer Access) git clone
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