monaLisa

DOI: 10.18129/B9.bioc.monaLisa    

Binned Motif Enrichment Analysis and Visualization

Bioconductor version: Release (3.14)

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] , Lukas Burger [aut], Charlotte Soneson [aut] , Michael Stadler [aut, cre]

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

Installation

To install this package, start R (version "4.1") 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")

 

HTML	R Script	monaLisa - MOtif aNAlysis with Lisa
HTML	R Script	selecting_motifs_with_randLassoStabSel
PDF		Reference Manual
Text		NEWS

Details

biocViews	Epigenetics, FeatureExtraction, MotifAnnotation, Software, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.14 (R-4.1) (< 6 months)
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(>= 2.0.0), XVector, GenomeInfoDb, tools, vioplot
LinkingTo
Suggests	JASPAR2020, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra
SystemRequirements
Enhances
URL	https://github.com/fmicompbio/monaLisa https://bioconductor.org/packages/monaLisa/ https://fmicompbio.github.io/monaLisa/
BugReports	https://github.com/fmicompbio/monaLisa/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	monaLisa_1.0.0.tar.gz
Windows Binary	monaLisa_1.0.0.zip
macOS 10.13 (High Sierra)	monaLisa_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/monaLisa
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/monaLisa
Package Short Url	https://bioconductor.org/packages/monaLisa/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive