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")):
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")
## The following initializes the development version of Bioconductor
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 | 1.31.46 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | GPL-3 |
| Depends | R (>= 4.1.0) |
| Imports | methods, stats, utils, parallel, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, grDevices, 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, 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_1.31.46.tar.gz |
| Windows Binary (x86_64) | universalmotif_1.31.46.zip |
| macOS Binary (big-sur-x86_64) | universalmotif_1.31.46.tgz |
| macOS Binary (sonoma-arm64) | universalmotif_1.31.46.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 |