universalmotif
This is the development version of universalmotif; for the stable release version, see universalmotif.
Import, Modify, and Export Motifs with R
Bioconductor version: Development (3.24)
A comprehensive toolkit for working with sequence motifs in R. Imports and exports most common motif formats (JASPAR, MEME, HOMER, TRANSFAC, CIS-BP, UNIPROBE) and interoperates with the other Bioconductor motif packages. Analysis functions cover de novo motif discovery, motif-vs-motif comparison and clustering, P-value calculation, sequence scanning, enrichment against shuffled or composition-matched backgrounds, positional bias testing, and pairwise motif co-occurrence. Also includes utilities for sequence shuffling, motif trimming, higher-order representations, ground-truth simulation by motif implantation, and logo-plotting functionality.
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 "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")| An end-to-end ChIP-seq workflow | R Script | |
| Building a curated motif database | 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, GeneRegulation, MotifAnnotation, MotifDiscovery, Software |
| Version | 1.31.32 |
| In Bioconductor since | BioC 3.8 (R-3.5) (7.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1.0) |
| Imports | methods, stats, utils, parallel, 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, GenomeInfoDb, ggbio, rtracklayer, BSgenome.Athaliana.TAIR.TAIR9 |
| Linking To | Rcpp, RcppThread |
| Enhances | PWMEnrich, rGADEM |
| Depends On Me | |
| Imports Me | ChIPpeakAnno, circRNAprofiler, memes, MotifPeeker, SEMPLR |
| Suggests Me | epiSeeker |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | universalmotif_1.31.32.tar.gz |
| Windows Binary (x86_64) | universalmotif_1.31.32.zip |
| macOS Binary (big-sur-x86_64) | universalmotif_1.31.32.tgz |
| macOS Binary (sonoma-arm64) | universalmotif_1.31.32.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 |