SuRFing the genomics wave: an R package for prioritising SNPs by functionality

Identifying functional non-coding variants is one of the greatest unmet challenges in genetics. To help address this, we introduce an R package, SuRFR, which integrates functional annotation and prior biological knowledge to prioritise candidate functional variants. SuRFR is publicly available, modu...

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Detalles Bibliográficos
Autores principales: Ryan, Niamh M, Morris, Stewart W, Porteous, David J, Taylor, Martin S, Evans, Kathryn L
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224693/
https://www.ncbi.nlm.nih.gov/pubmed/25400697
http://dx.doi.org/10.1186/s13073-014-0079-1
Descripción
Sumario:Identifying functional non-coding variants is one of the greatest unmet challenges in genetics. To help address this, we introduce an R package, SuRFR, which integrates functional annotation and prior biological knowledge to prioritise candidate functional variants. SuRFR is publicly available, modular, flexible, fast, and simple to use. We demonstrate that SuRFR performs with high sensitivity and specificity and provide a widely applicable and scalable benchmarking dataset for model training and validation. Website: http://www.cgem.ed.ac.uk/resources/ ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13073-014-0079-1) contains supplementary material, which is available to authorized users.

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