About decompTumor2Sig

The decompTumor2Sig R package uses quadratic programming to decompose the mutation catalog from an individual tumor sample (or multiple individual tumor samples) into a set of given mutational signatures (either the Alexandrov model or the Shiraishi model), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.

The package additionally provides helper functions to extract genomes (mutation catalogs) and signatures from objects provided by pmsignature or to read them from files.

Citing decompTumor2Sig: please cite Krüger S, Piro RM (2017) Identification of Mutational Signatures Active in Individual Tumors. NETTAB 2017 - Methods, Tools & Platforms for Personalized Medicine in the Big Data Era, October 16-18, 2017, Palermo, Italy.


Downloads

decompTumor2Sig version 1.0 (Krüger;, Piro 2017):

Dendencies: R, Matrix, quadpog
Recommended: pmsignature
Version 1.0 provides a function to compute signature weights in individual tumor genomes and additional functions to extract mutation information and singature information from objects generated using pmsignature's methods.


Publications

Identification of Mutational Signatures Active in Individual Tumors

NETTAB 2017 - Methods, Tools & Platforms for Personalized Medicine in the Big Data Era, October 16-18, 2017, Palermo, Italy.

Sandra Krüger (1), Rosario M. Piro (1,2,3,*)

(1) Institute of Computer Science and Institute of Bioinformatics, Freie Universität Berlin, Berlin, Germany
(2) Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
(3) German Cancer Consortium (DKTK)
(*) corresponding author: r.piro -AT- fu-berlin.de or rmpiro -AT- gmail.com

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Contact

For questions regarding decompTumor2Sig, please write to:

Prof. Dr. Rosario M. Piro

Dep. of Mathematics and Computer Science
Institute of Computer Science
Freie Universität Berlin
Takustr. 9
14195 Berlin, Germany
Phone: +49 (0)30 838 55114

E-mail: r.piro -AT- fu-berlin.de

Or contact Prof. Dr. Rainer König at HKI!


Impressum/Legal notice according to German legislation

Responsible for the content of this website according to
§ 5 TMG (German Act for Telecommunications Media Services)
and § 55 Abs. 2 RStV (German Interstate Broadcasting Agreement):

Prof. Dr. Rosario M. Piro
Dep. of Mathematics and Computer Science
Freie Universität Berlin
Takustr. 9
14195 Berlin, Germany
E-mail: r.piro -AT- fu-berlin.de

Liability for the content of linked websites:
This website contains links to external websites on whose content I have no influence and for which I thus cannot take any responsibility. The responsibility for the content of linked websites lies with the providers or administrators of the respective websites. Linked websites have been checked for a possible infringement of laws upon creation of the link. No infringement could be identified when the links were created. A permanent control of the content of the linked websites is not reasonable without a tangible suspicion of the violation of a law. If I should be notified or otherwise become aware of violations of law by the content of a linked website, I will immediately remove the corresponding link.

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