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>

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

Installation

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

if (!requireNamespace("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

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