PWMEnrich
PWM enrichment analysis
Bioconductor version: 3.24 · Package version: 4.49.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PWMEnrich")Details
| Maintainer | Diego Diez <diego10ruiz@gmail.com> |
| Author | Robert Stojnic, Diego Diez |
| License | LGPL (>= 2) |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | MotifAnnotation, SequenceMatching, Software |
| Package Short Url | https://bioconductor.org/packages/PWMEnrich/ |
Citation
From within R, enter citation("PWMEnrich"):
Robert Stojnic, Diego Diez. PWMEnrich: PWM enrichment analysis. doi:10.18129/B9.bioc.PWMEnrich, R package version 4.49.0, https://bioconductor.org/packages/PWMEnrich.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | PWMEnrich_4.49.0.tar.gz |
| Windows binary (x86_64) | PWMEnrich_4.49.0.zip |
| macOS binary (arm64) | PWMEnrich_4.49.0.tgz |
| macOS binary (x86_64) | PWMEnrich_4.49.0.tgz |
Dependencies
Depends: R (>= 3.5.0), methods, BiocGenerics, Biostrings
Imports: grid, seqLogo, gdata, evd, S4Vectors
Suggests: MotifDb, BSgenome, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr
Reverse dependencies
Depends On Me (3): PWMEnrich.Dmelanogaster.background, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background
Suggests Me (1): rTRM