Package: motifbreakR 2.19.0

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]

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motifbreakR.pdf |motifbreakR.html✨
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# Install 'motifbreakR' in R:

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

The latest version of this package failed to build. Look at thebuild logs for more information.

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-2.19.0(bioc 3.20)motifbreakR-2.18.0(bioc 3.19)

bioconductor-package

7 exports 1.31 score 176 dependencies 13 mentions

Last updated 2 months agofrom:b35745f9d7

Exports:calculatePvalue exportMBresults motifbreakR plotMB snps.from.file snps.from.rsid variants.from.file

Dependencies:abind ade4 annotate AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem caTools checkmate cli clipr cluster CNEr codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest DirichletMultinomial dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue GO.db gridExtra gtable gtools Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime MotifDb motifStack munsell nlme nnet openssl pillar pixmap pkgconfig plogr plyr png poweRlaw pracma prettyunits progress ProtGenerics purrr pwalign R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl readr reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales seqLogo snow sp SparseArray splitstackshape stringi stringr SummarizedExperiment sys TFBSTools TFMPvalue tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc

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

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
MotifDb object containing motif information from around the genomic regions bound by 119 human transcription factors in Factorbook.	factorbook
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
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 2.19.0

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

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