monaLisa

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

Binned Motif Enrichment Analysis and Visualization

Bioconductor version: Development (3.21)

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: ), Lukas Burger [aut] (ORCID: ), Charlotte Soneson [aut] (ORCID: ), Dany Mukesha [ctb] (ORCID: ), Michael Stadler [aut, cre] (ORCID: )

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")

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	1.13.0
In Bioconductor since	BioC 3.14 (R-4.1) (3 years)
License	GPL (>= 3)
Depends	R (>= 4.1)
Imports	methods, stats, utils, grDevices, graphics, BiocGenerics, GenomicRanges, TFBSTools, Biostrings, IRanges, stabs, BSgenome, glmnet, S4Vectors, SummarizedExperiment, BiocParallel, grid, circlize, ComplexHeatmap(>= 2.11.1), XVector, GenomeInfoDb, tools, vioplot, RSQLite
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	JASPAR2020, JASPAR2024, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra
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.

Source Package	monaLisa_1.13.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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/
Package Downloads Report	Download Stats