Package: monaLisa
Type: Package
Title: Binned Motif Enrichment Analysis and Visualization
Version: 1.16.0
Authors@R: c(
    person("Dania", "Machlab", email = "dania.machlab@gmail.com", role = c("aut"), 
           comment = c(ORCID = "0000-0002-2578-6930")),
    person("Lukas", "Burger", email = "lukas.burger@fmi.ch", role = c("aut"),
           comment = c(ORCID = "0000-0001-5596-7567")),
    person("Charlotte", "Soneson", email = "charlottesoneson@gmail.com", 
           role = c("aut"),
           comment = c(ORCID = "0000-0003-3833-2169")),
    person("Dany", "Mukesha", role = c("ctb"),
           comment = c(ORCID = "0009-0001-9514-751X")),
    person("Michael", "Stadler", email = "michael.stadler@fmi.ch", 
           role = c("aut", "cre"), comment = c(ORCID = "0000-0002-2269-4934")))
Description: 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.
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
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.3.2
VignetteBuilder: knitr
biocViews: MotifAnnotation, Visualization, FeatureExtraction,
        Epigenetics
Config/testthat/edition: 3
URL: https://github.com/fmicompbio/monaLisa,
        https://bioconductor.org/packages/monaLisa/,
        https://fmicompbio.github.io/monaLisa/
BugReports: https://github.com/fmicompbio/monaLisa/issues
Config/pak/sysreqs: make libgsl0-dev libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev perl xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:12:31 UTC
RemoteUrl: https://github.com/bioc/monaLisa
RemoteRef: RELEASE_3_22
RemoteSha: fb7bf5b04b784c53ab4405e46d1fdf52d4177028
NeedsCompilation: no
Packaged: 2026-01-28 08:53:52 UTC; root
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>)
Maintainer: Michael Stadler <michael.stadler@fmi.ch>
Built: R 4.5.2; ; 2026-01-28 08:56:57 UTC; windows
