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sequenza  

Copy Number Estimation from Tumor Genome Sequencing Data
View on CRAN: Click here


Download and install sequenza package within the R console
Install from CRAN:
install.packages("sequenza")

Install from Github:
library("remotes")
install_github("cran/sequenza")

Install by package version:
library("remotes")
install_version("sequenza", "3.0.0")



Attach the package and use:
library("sequenza")
Maintained by
Francesco Favero
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2013-12-02
Latest Update: 2023-04-01
Description:
Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
How to cite:
Francesco Favero (2013). sequenza: Copy Number Estimation from Tumor Genome Sequencing Data. R package version 3.0.0, https://cran.r-project.org/web/packages/sequenza
Previous versions and publish date:
1.0.1 (2013-12-02 21:34), 1.0.2 (2013-12-05 00:39), 1.0.3 (2013-12-12 12:53), 1.0.4 (2014-01-20 07:20), 1.0.5 (2014-02-11 15:24), 2.0.0 (2014-04-08 07:02), 2.1.0 (2014-10-08 17:22), 2.1.1 (2015-01-27 16:55), 2.1.2 (2015-10-10 01:22), 3.0.0 (2019-05-09 15:50)
Other packages that cited sequenza R package
View sequenza citation profile
Other R packages that sequenza depends, imports, suggests or enhances
Functions, R codes and Examples using the sequenza R package
Some associated functions: CP.data . baf.model.fit . bayes . breaks . chromosome.view . cp.plot . example.seqz . gc . model_points . mutations . plotWindows . read_seqz . theoretical . type_matrix . windowValues . workflow . 
Some associated R codes: bayes.R . extract.R . fit.R . gcstats.R . graphics.R . misc.R . model.R . mutations.R . read.R . results.R . segments.R . solutions.R . windows.R .  Full sequenza package functions and examples
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