Package: motifbreakR 2.27.2

Simon Gert Coetzee

motifbreakR: A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

We introduce motifbreakR, which allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. MotifbreakR is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum probability matrix, 2) log-probabilities, and 3) weighted by relative entropy. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor (currently there are 32 species, a total of 109 versions).

Authors:Simon Gert Coetzee [aut, cre], Dennis J. Hazelett [aut]

motifbreakR_2.27.2.tar.gz
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motifbreakR_2.27.2.tgz(r-4.6-any)motifbreakR_2.27.2.tgz(r-4.5-any)
motifbreakR_2.27.2.tar.gz(r-4.7-any)motifbreakR_2.27.2.tar.gz(r-4.6-any)
motifbreakR_2.27.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
motifbreakR/json (API)

# Install 'motifbreakR' in R:

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

Bug tracker:https://github.com/simon-coetzee/motifbreakr/issues

Datasets:

encodemotif - MotifDb object containing motif information from the known and discovered motifs for the ENCODE TF ChIP-seq datasets.
example.results - Example Results from motifbreakR
factorbook - MotifDb object containing motif information from around the genomic regions bound by 119 human transcription factors in Factorbook.
hocomoco - MotifDb object containing motif information from Homo Sapiens Comprehensive Model Collection (HOCOMOCO) of transcription factor (TF) binding models
homer - MotifDb object containing motif information from motif databases included in HOMER.
motifbreakR_motif - MotifDb object containing motif information from the motif databases of HOCOMOCO, Homer, FactorBook and ENCODE

On BioConductor:motifbreakR-2.27.2(bioc 3.24)motifbreakR-2.26.0(bioc 3.23)

chipseq visualization motifannotation transcription

8.38 score 34 stars 157 scripts 13 mentions 10 exports 170 dependencies

Last updated from:21d39f8cc6. Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	524
linux-devel-x86_64	ERROR	867
source / vignettes	ERROR	662
linux-release-x86_64	ERROR	844
macos-release-arm64	ERROR	533
macos-oldrel-arm64	ERROR	471
windows-devel	ERROR	707
windows-release	ERROR	733
windows-oldrel	ERROR	681
wasm-release	OK	473

Exports:calculatePvalue exportMBbed exportMBtable findSupportingRemapPeaks motifbreakR plotMB shiny_motifbreakR snps.from.file snps.from.rsid variants.from.file

Dependencies:abind ade4 AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bsicons bslib cachem caTools checkmate cigarillo cli cluster codetools colorspace commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir dichromat digest DirichletMultinomial dplyr DT ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable gtools Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime MotifDb motifStack nnet openssl otel pillar pixmap pkgconfig png prettyunits progress promises ProtGenerics purrr pwalign R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo seqLogo shiny snow sourcetools sp SparseArray splitstackshape stringi stringr SummarizedExperiment sys TFBSTools TFMPvalue tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 VariantAnnotation vctrs viridisLite vroom withr xfun XML xml2 xtable XVector yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

motifbreakR: an Introduction

Rendered frommotifbreakR-vignette.Rmdusingknitr::rmarkdown

Last update: 2026-05-18
Started: 2015-04-07

Help page	Topics
Calculate the significance of the matches for the reference and alternate alleles for the for their PWM	calculatePvalue
MotifDb object containing motif information from the known and discovered motifs for the ENCODE TF ChIP-seq datasets.	encodemotif
Example Results from motifbreakR	example.results
Export motifbreakR variants to bed file	exportMBbed
Export motifbreakR results to csv or tsv	exportMBtable
MotifDb object containing motif information from around the genomic regions bound by 119 human transcription factors in Factorbook.	factorbook
Find Corresponding TF Binding From The ReMap2022 Project	findSupportingRemapPeaks
MotifDb object containing motif information from Homo Sapiens Comprehensive Model Collection (HOCOMOCO) of transcription factor (TF) binding models	hocomoco
MotifDb object containing motif information from motif databases included in HOMER.	homer
Predict The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.	motifbreakR
MotifDb object containing motif information from the motif databases of HOCOMOCO, Homer, FactorBook and ENCODE	motifbreakR_motif
Plot a genomic region surrounding a genomic variant, and potentially disrupted motifs	plotMB
Run Shiny version of the motifbreakR package.	shiny_motifbreakR
Import SNPs from a BED file or VCF file for use in motifbreakR	snps.from.file variants.from.file
Import SNPs from rsid for use in motifbreakR	snps.from.rsid

Package: motifbreakR 2.27.2

motifbreakR: A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

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