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Bioconductor - monaLisa (development version)

monaLisa

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

Binned Motif Enrichment Analysis and Visualization

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-2578-6930 , Lukas Burger [aut] ORCID: 0000-0001-5596-7567 , Charlotte Soneson [aut] ORCID: 0000-0003-3833-2169 , Dany Mukesha [ctb] ORCID: 0009-0001-9514-751X , Michael Stadler [aut, cre] ORCID: 0000-0002-2269-4934

Maintainer: Michael Stadler <michael.stadler at fmi.ch>

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

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("monaLisa")

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

Documentation

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

browseVignettes("monaLisa")
Details biocViews Epigenetics, FeatureExtraction, MotifAnnotation, Software, Visualization Version 1.15.0 In Bioconductor since BioC 3.14 (R-4.1) (3.5 years) License GPL (>= 3) Depends R (>= 4.1) Imports BiocGenerics, BiocParallel, Biostrings, BSgenome, circlize, ComplexHeatmap(>= 2.11.1), GenomeInfoDb, GenomicRanges, cli, ggplot2, glmnet, grDevices, grid, IRanges, methods, rlang, RSQLite, stabs, stats, SummarizedExperiment, S4Vectors, TFBSTools, tidyr, tools, utils, XVector System Requirements URL https://github.com/fmicompbio/monaLisa https://bioconductor.org/packages/monaLisa/ https://fmicompbio.github.io/monaLisa/ Bug Reports https://github.com/fmicompbio/monaLisa/issues See More Suggests BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, ggrepel, gridExtra, JASPAR2020, JASPAR2024, knitr, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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