Bioconductor version: Release (3.11)
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 <b2tremblay at uwaterloo.ca>
Citation (from within R,
enter citation("universalmotif")
):
To install this package, start R (version "4.0") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("universalmotif")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("universalmotif")
R Script | 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 | |
Reference Manual | ||
Text | NEWS |
biocViews | DataImport, GeneRegulation, MotifAnnotation, MotifDiscovery, Software |
Version | 1.6.4 |
In Bioconductor since | BioC 3.8 (R-3.5) (2 years) |
License | GPL-3 |
Depends | R (>= 3.5.0) |
Imports | methods, stats, utils, MASS, ggplot2, ape, ggtree, ggseqlogo, yaml, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics, processx, S4Vectors, rlang |
LinkingTo | Rcpp, RcppThread |
Suggests | spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, Logolas, BiocParallel, seqLogo, motifStack, dplyr |
SystemRequirements | |
Enhances | MotIV, PWMEnrich, rGADEM, motifRG |
URL | https://github.com/bjmt/universalmotif |
BugReports | https://github.com/bjmt/universalmotif/issues |
Depends On Me | |
Imports Me | circRNAprofiler |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | universalmotif_1.6.4.tar.gz |
Windows Binary | universalmotif_1.6.4.zip (32- & 64-bit) |
macOS 10.13 (High Sierra) | universalmotif_1.6.4.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/universalmotif |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/universalmotif |
Package Short Url | https://bioconductor.org/packages/universalmotif/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.11 | Source Archive |
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