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:
Maintainer: Michael Stadler <michael.stadler at fmi.ch>
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 | ||
| NEWS | Text |
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 |
See More
| 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) | monaLisa_1.13.0.zip |
| 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 |