Package: motifTestR 1.3.3

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_1.3.3.tar.gz
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motifTestR.pdf |motifTestR.html✨
motifTestR/json (API)
NEWS

# 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-1.3.3(bioc 3.21)motifTestR-1.2.1(bioc 3.20)

motifannotation chipseq chiponchip sequencematching software

4.93 score 1 stars 2 scripts 179 downloads 12 exports 55 dependencies

Last updated 9 days agofrom:b1c54df338. Checks:7 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 20 2025
R-4.5-win	OK	Jan 20 2025
R-4.5-linux	OK	Jan 20 2025
R-4.4-win	OK	Jan 20 2025
R-4.4-mac	OK	Jan 20 2025
R-4.3-win	OK	Jan 20 2025
R-4.3-mac	OK	Jan 20 2025

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

Dependencies:askpass BiocGenerics Biostrings cli colorspace crayon curl fansi farver FMStable generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable harmonicmeanp httr IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl patchwork pillar pkgconfig R6 RColorBrewer Rcpp RcppThread rlang S4Vectors scales sys tibble UCSC.utils universalmotif utf8 vctrs viridisLite withr XVector yaml

Motif Analysis Using motifTestR

Stevie Pederson

Rendered frommotifAnalysis.Rmdusingknitr::rmarkdownon Jan 20 2025.

Last update: 2025-01-11
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 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