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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("motifbreakR")
In most cases, you don't need to download the package archive at all.
motifbreakR
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A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
Bioconductor version: Release (3.5)
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 22).
Author: Simon Gert Coetzee [aut, cre] Dennis J. Hazelett [aut]
Maintainer: Simon Gert Coetzee <Simon.Coetzee at cshs.org>
Citation (from within R,
enter citation("motifbreakR")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("motifbreakR")
Documentation
| HTML | R Script | motifbreakR: an Introduction |
| Reference Manual |
Details
| biocViews | ChIPSeq, MotifAnnotation, Software, Visualization |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (2 years) |
| License | GPL-2 |
| Depends | R (>= 3.2), grid, MotifDb |
| Imports | methods, compiler, grDevices, grImport, stringr, BiocGenerics, S4Vectors(>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue |
| LinkingTo | |
| Suggests | BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP142.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle |
| SystemRequirements | |
| Enhances | |
| URL | |
| BugReports | https://github.com/Simon-Coetzee/motifbreakR/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | motifbreakR_1.6.0.tar.gz |
| Windows Binary | motifbreakR_1.6.0.zip |
| Mac OS X 10.11 (El Capitan) | motifbreakR_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/motifbreakR |
| Package Short Url | http://bioconductor.org/packages/motifbreakR/ |
| Package Downloads Report | Download Stats |
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