motifbreakR

MotifbreakR is a software tool designed to facilitate the functional annotation of germline and somatic variation revealed by genome-wide association studies (GWAS) and The Cancer Genome Atlas (TCGA). It allows users to assess the effects of variants on likely transcription factor binding sites and predict effects for novel or previously described variants in public databases. MotifbreakR is flexible and can be used to interrogate any genome curated within Bioconductor.

Topic

Sequence analysis;Nucleic acid sites, features and motifs;DNA polymorphism

Detail

  • Operation: Sequence motif analysis

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 2.12.3

  • Credit: The National Institutes of Healthand National Cancer Institute.

  • Input: -

  • Output: -

  • Contact: Simon Gert Coetzee Simon.Coetzee@cshs.org

  • Collection: -

  • Maturity: Mature

Publications

  • motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites.
  • Coetzee SG, et al. motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites. motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites. 2015; 31:3847-9. doi: 10.1093/bioinformatics/btv470
  • https://doi.org/10.1093/bioinformatics/btv470
  • PMID: 26272984
  • PMC: PMC4653394

Download and documentation

< Back to DB search