universalmotif
Import, Modify, and Export Motifs with R
Bioconductor version: Release (3.19)
Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.
Author: Benjamin Jean-Marie Tremblay [aut, cre] 
, Spencer Nystrom [ctb]
Maintainer: Benjamin Jean-Marie Tremblay <benjamin.tremblay at uwaterloo.ca>
citation("universalmotif")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("universalmotif")
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("universalmotif")| Introduction to "universalmotif" | R Script | |
| Introduction to sequence motifs | R Script | |
| Motif comparisons and P-values | R Script | |
| Motif import, export, and manipulation | R Script | |
| Sequence manipulation and scanning | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, GeneRegulation, MotifAnnotation, MotifDiscovery, Software |
| Version | 1.22.3 |
| In Bioconductor since | BioC 3.8 (R-3.5) (6 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0) |
| Imports | methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics |
| System Requirements | |
| URL | https://bioconductor.org/packages/universalmotif/ |
| Bug Reports | https://github.com/bjmt/universalmotif/issues |
See More
| Suggests | spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio |
| Linking To | Rcpp, RcppThread |
| Enhances | PWMEnrich, rGADEM |
| Depends On Me | |
| Imports Me | ChIPpeakAnno, circRNAprofiler, memes, motifTestR |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | universalmotif_1.22.3.tar.gz |
| Windows Binary (x86_64) | universalmotif_1.22.3.zip |
| macOS Binary (x86_64) | universalmotif_1.22.3.tgz |
| macOS Binary (arm64) | universalmotif_1.22.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/universalmotif |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/universalmotif |
| Bioc Package Browser | https://code.bioconductor.org/browse/universalmotif/ |
| Package Short Url | https://bioconductor.org/packages/universalmotif/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |