motifTestR
This is the development version of motifTestR; for the stable release version, see motifTestR.
Perform key tests for binding motifs in sequence data
Bioconductor version: Development (3.21)
Taking a set of sequence motifs as PWMs, test a set of sequences for over-representation of these motifs, as well as any positional features within the set of motifs. Enrichment analysis can be undertaken using multiple statistical approaches. The package also contains core functions to prepare data for analysis, and to visualise results.
Author: Stevie Pederson [aut, cre] (ORCID:
Maintainer: Stevie Pederson <stephen.pederson.au at gmail.com>
citation("motifTestR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("motifTestR")
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("motifTestR")| Motif Analysis Using motifTestR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, ChipOnChip, MotifAnnotation, SequenceMatching, Software |
| Version | 1.3.1 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| License | GPL-3 |
| Depends | Biostrings, GenomicRanges, ggplot2 (>= 3.5.0), R (>= 4.3.0) |
| Imports | GenomeInfoDb, graphics, harmonicmeanp, IRanges, matrixStats, methods, parallel, patchwork, rlang, S4Vectors, stats, universalmotif |
| System Requirements | |
| URL | https://github.com/smped/motifTestR |
| Bug Reports | https://github.com/smped/motifTestR/issues |
See More
| Suggests | AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs, ggdendro, knitr, MotifDb, rmarkdown, rtracklayer, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | motifTestR_1.3.1.tar.gz |
| Windows Binary (x86_64) | motifTestR_1.3.1.zip |
| macOS Binary (x86_64) | motifTestR_1.3.1.tgz |
| macOS Binary (arm64) | motifTestR_1.3.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/motifTestR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/motifTestR |
| Bioc Package Browser | https://code.bioconductor.org/browse/motifTestR/ |
| Package Short Url | https://bioconductor.org/packages/motifTestR/ |
| Package Downloads Report | Download Stats |