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monaLisa

Binned Motif Enrichment Analysis and Visualization

Bioconductor version: 3.24 · Package version: 1.19.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("monaLisa")

Details

MaintainerMichael Stadler <michael.stadler@fmi.ch>
AuthorDania Machlab [aut] (ORCID: <https://orcid.org/0000-0002-2578-6930>), Lukas Burger [aut] (ORCID: <https://orcid.org/0000-0001-5596-7567>), Charlotte Soneson [aut] (ORCID: <https://orcid.org/0000-0003-3833-2169>), Dany Mukesha [ctb] (ORCID: <https://orcid.org/0009-0001-9514-751X>), Michael Stadler [aut, cre] (ORCID: <https://orcid.org/0000-0002-2269-4934>)
LicenseGPL (>= 3)
URLhttps://github.com/fmicompbio/monaLisa, https://bioconductor.org/packages/monaLisa/, https://fmicompbio.github.io/monaLisa/
Bug Reportshttps://github.com/fmicompbio/monaLisa/issues
Downloads rank660
Source branchdevel
biocViewsEpigenetics, FeatureExtraction, MotifAnnotation, Software, Visualization

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packagemonaLisa_1.19.0.tar.gz
Windows binary (x86_64)monaLisa_1.19.0.zip
macOS binary (arm64)monaLisa_1.19.0.tgz
macOS binary (x86_64)monaLisa_1.19.0.tgz
Dependencies

Depends: R (>= 4.1)

Imports: BiocGenerics, BiocParallel, Biostrings, BSgenome, circlize, ComplexHeatmap (>= 2.11.1), Seqinfo, GenomicRanges, cli, ggplot2 (>= 4.0.0), glmnet, grDevices, grid, IRanges, methods, rlang, RSQLite, stabs, stats, SummarizedExperiment, S4Vectors, TFBSTools, tidyr, tools, utils, XVector

Suggests: BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, ggrepel, gridExtra, JASPAR2020, JASPAR2024, knitr, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene