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Bioinformatics. 2015 Nov 15;31(22):3673-5. doi: 10.1093/bioinformatics/btv408. Epub 2015 Jul 10.

SomaticSignatures: inferring mutational signatures from single-nucleotide variants.

Author information

1
European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany, Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA and.
2
European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany, Computational Genome Biology, German Cancer Research Center, 69120 Heidelberg, Germany.
3
Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA and.
4
European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.

Abstract

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.

PMID:
26163694
PMCID:
PMC4817139
DOI:
10.1093/bioinformatics/btv408
[Indexed for MEDLINE]
Free PMC Article

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