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SomaticSignatures: inferring mutational signatures from single-nucleotide variants

Summary: Mutational signatures are patterns in the occurrence of somatic single-nucleotide variants that can reflect underlying mutational processes. The SomaticSignatures package provides flexible, interoperable and easy-to-use tools that identify such signatures in cancer sequencing data. It facil...

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Detalles Bibliográficos
Autores principales: Gehring, Julian S., Fischer, Bernd, Lawrence, Michael, Huber, Wolfgang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817139/
https://www.ncbi.nlm.nih.gov/pubmed/26163694
http://dx.doi.org/10.1093/bioinformatics/btv408
Descripción
Sumario:Summary: Mutational signatures are patterns in the occurrence of somatic single-nucleotide variants that can reflect underlying mutational processes. The SomaticSignatures package provides flexible, interoperable and easy-to-use tools that identify such signatures in cancer sequencing data. It facilitates large-scale, cross-dataset estimation of mutational signatures, implements existing methods for pattern decomposition, supports extension through user-defined approaches and integrates with existing Bioconductor workflows. Availability and implementation: The R package SomaticSignatures is available as part of the Bioconductor project. Its documentation provides additional details on the methods and demonstrates applications to biological datasets. Contact: julian.gehring@embl.de, whuber@embl.de Supplementary information: Supplementary data are available at Bioinformatics online.