Package: motifTestR 1.9.0

Stevie Pederson

motifTestR: Perform key tests for binding motifs in sequence data

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.

Authors:Stevie Pederson [aut, cre]

motifTestR_1.9.0.tar.gz
motifTestR_1.9.0.zip(r-4.7)motifTestR_1.9.0.zip(r-4.6)motifTestR_1.9.0.zip(r-4.5)
motifTestR_1.9.0.tgz(r-4.6-any)motifTestR_1.9.0.tgz(r-4.5-any)
motifTestR_1.9.0.tar.gz(r-4.7-any)motifTestR_1.9.0.tar.gz(r-4.6-any)
motifTestR_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
motifTestR/json (API)

# Install 'motifTestR' in R:

install.packages('motifTestR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/smped/motiftestr/issues

Datasets:

ar_er_peaks - A set of peaks with AR and ER detected
ar_er_seq - Sequences from peaks with AR and ER detected
ex_pfm - Example Position Frequency Matrices
hg19_mask - Regions from hg19 with high N content
zr75_enh - Candidate Enhancer Regions from ZR-75-1 Cells

On BioConductor:motifTestR-1.9.0(bioc 3.24)motifTestR-1.8.0(bioc 3.23)

motifannotation chipseq chiponchip sequencematching software

4.90 score 1 stars 3 scripts 13 exports 36 dependencies

Last updated from:ee8914c9e3. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	235
linux-devel-x86_64	OK	396
source / vignettes	OK	378
linux-release-x86_64	OK	394
macos-release-arm64	OK	332
macos-oldrel-arm64	OK	240
windows-devel	OK	278
windows-release	OK	300
windows-oldrel	OK	298
wasm-release	OK	238

Exports:clusterMotifs countClusterMatches countPwmMatches getClusterMatches getPwmMatches makeRMRanges plotMatchPos simMultiMotifs simSeq testClusterEnrich testClusterPos testMotifEnrich testMotifPos

Dependencies:BiocGenerics Biostrings cli cpp11 crayon farver FMStable generics GenomicRanges ggplot2 glue gtable harmonicmeanp IRanges isoband labeling lifecycle MASS MatrixGenerics matrixStats patchwork R6 RColorBrewer Rcpp RcppThread rlang S4Vectors S7 scales Seqinfo universalmotif vctrs viridisLite withr XVector yaml

Motif Analysis Using motifTestR

Rendered frommotifAnalysis.Rmdusingknitr::rmarkdown

Last update: 2025-10-03
Started: 2024-02-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A set of peaks with AR and ER detected	ar_er_peaks
Sequences from peaks with AR and ER detected	ar_er_seq
Assign each motif to a cluster	clusterMotifs
Count the matches to a PWM within an XStringSet	countPwmMatches
Example Position Frequency Matrices	ex_pfm
Find matches from a PWM cluster within an XStringSet	countClusterMatches getClusterMatches
Find all PWM matches within an XStringSet	getPwmMatches
Regions from hg19 with high N content	hg19_mask
Form a set of random, matching ranges for bootstrapping or permuting	makeRMRanges makeRMRanges,GRanges,GRanges-method makeRMRanges,GRangesList,GRangesList-method
Plot Motif Match Positions	plotMatchPos
Simulate sequences with multiple motifs	simMultiMotifs
Simulate sequences using optional TFBMs	simSeq
Test enrichment across a cluster of motifs using a background set of sequences	testClusterEnrich
Test positional bias motifs within a cluster	testClusterPos
Test motif enrichment using a background set of sequences	testMotifEnrich
Test for a Uniform Distribution across a set of best matches	testMotifPos
Candidate Enhancer Regions from ZR-75-1 Cells	zr75_enh