universalmotif

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see universalmotif.

Import, Modify, and Export Motifs with R

Bioconductor version: 3.10

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]

Maintainer: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>

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

Installation

To install this package, start R (version "3.6") 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" PDF R Script

Introduction to sequence motifs PDF R Script

Motif comparisons and P-values PDF R Script

Motif import, export, and manipulation PDF R Script

Sequence manipulation and scanning PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, GeneRegulation, MotifAnnotation, MotifDiscovery, Software

Version 1.4.10

In Bioconductor since BioC 3.8 (R-3.5) (5.5 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

System Requirements

URL https://github.com/bjmt/universalmotif

Bug Reports https://github.com/bjmt/universalmotif/issues

Suggests spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, Logolas, BiocParallel, seqLogo, motifStack, dplyr

Linking To Rcpp, RcppThread

Enhances MotIV, PWMEnrich, rGADEM, motifRG

Depends On Me

Imports Me

Suggests Me

Links To Me

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