motifTestR

This is the released version of motifTestR; for the devel version, see motifTestR.

Perform key tests for binding motifs in sequence data

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DOI: 10.18129/B9.bioc.motifTestR

Bioconductor version: Release (3.22)

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 iD ORCID: 0000-0001-8197-3303

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

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ChIPSeq, ChipOnChip, MotifAnnotation, SequenceMatching, Software

Version 1.6.0

In Bioconductor since BioC 3.19 (R-4.4) (1.5 years)

License GPL-3

Depends Biostrings, GenomicRanges, ggplot2 (>= 4.0.0), R (>= 4.5.0)

Imports Seqinfo, 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

Suggests AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs(>= 1.13.3), ggdendro, knitr, MASS, MotifDb, rmarkdown, rtracklayer, SimpleUpset, testthat (>= 3.0.0), VGAM

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Package Archives

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

Source Package motifTestR_1.6.0.tar.gz

Windows Binary (x86_64) motifTestR_1.5.1.zip

macOS Binary (x86_64) motifTestR_1.6.0.tgz

macOS Binary (arm64) motifTestR_1.6.0.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/

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