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Sequenza - Analyzing cancer NGS sequencing data

Sequenza

Sequenza

cancer NGS data analysis

Sequenza is a novel set of tools providing a fast python script to genotype cancer samples, and an R package to estimate cancer cellularity, ploidy, genome wide copy number profile and infer for mutated alleles.

Cite sequenza

F. Favero, T. Joshi,A. M. Marquard, N. J. Birkbak, M. Krzystanek, Q. Li, Z. Szallasi, and A. C. Eklund. “Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data”. Annals of Oncology, 2015, vol. 26, issue 1, 64-70.

sequenza R package

Sequenza at CRAN
Source code on Bitbucket

sequenza-utils Python

part of the R package
Development on Bitbucket

Getting Help

Mailing list at Google Groups - Wiki - User Guide

Cellularity and ploidy estimation

The cellularity and ploidy values of the sample are estimated trough Bayesian inference. The results can be expressed in a selected confidence region (C.R.) and one point estimate.

Copy number and mutations profile

The sequenza R package uses the estimated value of cellularity and ploidy to fit the data into the built-in model, estimating copy number and mutated allele from the data. Furthermore the package provides very intuitive, yet information rich graphics

Genome wide profiling

Copy number and allele composition, genome wide profiles



GETTING HELP

Contact: :       

This file was last modified Monday 20th 2016f June 2016 13:07:26 GMT