universalmotif
Import, Modify, and Export Motifs with R
Bioconductor version: 3.23 · Package version: 1.30.1
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("universalmotif") Details
| Maintainer | Benjamin Jean-Marie Tremblay <benjamin.tremblay@uwaterloo.ca> |
| Author | Benjamin Jean-Marie Tremblay [aut, cre] (ORCID: <https://orcid.org/0000-0002-7441-2951>), Spencer Nystrom [ctb] (ORCID: <https://orcid.org/0000-0003-1000-1579>) |
| License | GPL-3 |
| URL | https://bioconductor.org/packages/universalmotif/ |
| Bug Reports | https://github.com/bjmt/universalmotif/issues |
| Downloads rank | 1559 |
| Source branch | RELEASE_3_23 |
| biocViews | DataImport, GeneRegulation, MotifAnnotation, MotifDiscovery, Software |
Documentation
- Introduction to "universalmotif"
- Introduction to sequence motifs
- Motif comparisons and P-values
- Motif import, export, and manipulation
- Sequence manipulation and scanning
Download
Dependencies
Depends: R (>= 4.1.0)
Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics
LinkingTo: Rcpp, RcppThread
Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio
Reverse dependencies
Imports Me (6): ChIPpeakAnno, circRNAprofiler, memes, MotifPeeker, motifTestR, SEMPLR
Suggests Me (1): epiSeeker