universalmotif
This is the released version of universalmotif; for the devel version, see universalmotif.
Import, Modify, and Export Motifs with R
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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" | 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 | 1.30.1 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | GPL-3 |
| Depends | R (>= 4.1.0) |
| 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, 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_1.30.1.tar.gz |
| Windows Binary (x86_64) | universalmotif_1.30.1.zip |
| macOS Binary (big-sur-x86_64) | universalmotif_1.30.1.tgz |
| macOS Binary (sonoma-arm64) | universalmotif_1.30.1.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 3.23 | Source Archive |