monaLisa

Binned Motif Enrichment Analysis and Visualization

Bioconductor version: 3.23 · Package version: 1.18.0

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

Maintainer	Michael Stadler <michael.stadler@fmi.ch>
Author	Dania 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>)
License	GPL (>= 3)
URL	https://github.com/fmicompbio/monaLisa, https://bioconductor.org/packages/monaLisa/, https://fmicompbio.github.io/monaLisa/
Bug Reports	https://github.com/fmicompbio/monaLisa/issues
Downloads rank	439
Source branch	RELEASE_3_23
biocViews	Epigenetics, FeatureExtraction, MotifAnnotation, Software, Visualization

Documentation

Download

Source package

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