Sequenza

Sequenza package provides tools to genotyping cancer samples, cancer cellularity, ploidy, copy number variation (CNV), and infer alleles that are mutated.

Topic

Genetics; DNA structural variation; Oncology

Details

Operation: Polymorphism detection; Sequence analysis; Structural variation detection
Software interface: Command-line user interface; Library
Language: R:Python
Operating system: Microsoft Windows, Mac OS X, Linux
License: GNU General Public License v3

Cost

Version name: 3.0.0

Maturity:

Credit: The European Commission 7th Framework Programme, the Danish Council for Independent Research.
Contact: favero.francesco at gmail.com
Collection: -

Publications

Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC "Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data." Ann Oncol. 2015 Jan;26(1):64-70. https://doi.org/10.1093/annonc/mdu479
PMID: 25319062
PMCID: PMC4269342

Download and documentation

Source: http://www.cbs.dtu.dk/biotools/sequenza/
Documentation: https://cran.r-project.org/web/packages/
sequenza/vignettes/sequenza.html
Home page: http://www.cbs.dtu.dk/biotools/sequenza/
Links: https://cran.r-project.org/web/packages/
sequenza/sequenza.pdf

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Sequenza

Sequenza

Topic

Details

Publications

Download and documentation

TOOLS

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