monaLisa

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see monaLisa.

Binned Motif Enrichment Analysis and Visualization

Bioconductor version: 3.21

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

monaLisa - MOtif aNAlysis with Lisa HTML R Script

selecting_motifs_with_randLassoStabSel HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Epigenetics, FeatureExtraction, MotifAnnotation, Software, Visualization

Version 1.14.1

In Bioconductor since BioC 3.14 (R-4.1) (4 years)

License GPL (>= 3)

Depends R (>= 4.1)

Imports BiocGenerics, BiocParallel, Biostrings, BSgenome, circlize, ComplexHeatmap(>= 2.11.1), GenomeInfoDb, GenomicRanges, cli, ggplot2 (>= 4.0.0), 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

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

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Package Archives

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

Source Package monaLisa_1.14.1.tar.gz

Windows Binary (x86_64) monaLisa_1.14.0.zip

macOS Binary (x86_64) monaLisa_1.14.1.tgz

macOS Binary (arm64) monaLisa_1.14.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/monaLisa

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/monaLisa

Bioc Package Browser https://code.bioconductor.org/browse/monaLisa/

Package Short Url https://bioconductor.org/packages/monaLisa/

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Old Source Packages for BioC 3.21 Source Archive