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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 (3.20)

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]

Maintainer: Stevie Pederson <stephen.pederson.au at gmail.com>

Citation (from within R, enter citation("motifTestR")):

Installation

To install this package, start R (version "4.4") 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 PDF
NEWS Text

Details

biocViews ChIPSeq, ChipOnChip, MotifAnnotation, SequenceMatching, Software
Version 1.1.3
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL-3
Depends Biostrings, GenomicRanges, ggplot2 (>= 3.5.0), R (>= 4.3.0)
Imports GenomeInfoDb, 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
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package motifTestR_1.1.3.tar.gz
Windows Binary motifTestR_1.1.3.zip
macOS Binary (x86_64) motifTestR_1.1.3.tgz
macOS Binary (arm64) motifTestR_1.1.3.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