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:

Krüger S, Piro RM. decompTumor2Sig: Identification of mutational signatures active in individual tumors. BMC Bioinformatics 20(Suppl 4):152, 2019.

Download

decompTumor2Sig (since version 2.0.0):

Since version 2.0.0, decompTumor2Sig is part of Bioconductor (version 3.9+)!

Please download and install decompTumor2Sig via Bioconductor:

https://www.bioconductor.org/packages/release/bioc/html/decompTumor2Sig.html

[The following legacy package versions are obsolete:]

decompTumor2Sig version 1.99.1 (7 April 2019):

Dendencies: R, ggplot2, methods, Matrix, quadprog(>= 1.5-5), vcfR, GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table

Recommended: knitr, rmarkdown, BiocStyle

Version 1.99.1 (numbering increased to x.99 for submission to Bioconductor) improves the handling of MPF mutation files containing a large set of tumor genomes, the handling of somatic mutations in regions with overlapping genes of opposing transcription directions (when the transcritpion direction is considered), and fixes some minor problems.

decompTumor2Sig version 1.3.3 (24 September 2018):

Dendencies: R, ggplot2, methods, Matrix, quadprog(>= 1.5-5), vcfR, GenomicRanges, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, plyr, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra

Recommended: pmsignature, knitr, rmarkdown, BiocStyle

Version 1.3.3 provides new implementations of the plot functions that work with CRAN and Bioconductor dependencies alone, and additional functions to check signature formats, etc.

decompTumor2Sig version 1.3.0 (26 July 2018):

Recommended: pmsignature, knitr, rmarkdown, BiocStyle

Version 1.3 provides several new functions, e.g, for comparing signatures and converting them to different types.

decompTumor2Sig version 1.2 (4 March 2018):

Dendencies: R, Matrix, quadprog, vcfR, GenomicRanges, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr

Recommended: pmsignature

Version 1.2 provides a function to compute signature weights in individual tumor genomes and additional functions to load mutation information and signature information or to extract them from objects generated using pmsignature's methods. It provides functions to plot the results and evaluate the minimum number of signatures required to explain a certain variance of the mutational patterns observed in a tumor genome.

decompTumor2Sig version 1.0 (September 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.

R package decompTumor2Sig v1.0.0 (Linux)

Publications

Publications describing the decompTumor2Sig package:

decompTumor2Sig: Identification of mutational signatures active in individual tumors

(Please use this article for citing decompTumor2Sig!)

BMC Bioinformatics 20(Suppl 4):152, 2019.
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

Identification of Mutational Signatures Active in Individual Tumors

PeerJ Preprints 5:e3257v1, 2017.
Proceedings of 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,*)

Contact

For questions about decompTumor2Sig, please write to:

Prof. Rosario M. Piro

Politecnico di Milano
Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB)
Via Ponzio 34/5
20133 Milano, Italy
Phone: +39 02 2399 3538

E-mail: rosariomichael.piro -AT- polimi.it
Institutional website: Piro @ DEIB

Impressum/Legal notice according to German legislation:

[This website is hosted in Germany...]

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. Rosario M. Piro
Politecnico di Milano
Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB)
Via Ponzio 34/5
20133 Milano, Italy
E-mail: rosariomichael.piro -AT- polimi.it

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.