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ioncopy  

Calling Copy Number Alterations in Amplicon Sequencing Data
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("ioncopy", "2.2.2")



Attach the package and use:
library("ioncopy")
Maintained by
Jan Budczies
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-08-26
Latest Update: 2020-08-11
Description:
Method for the calculation of copy numbers and calling of copy number alterations. The algorithm uses coverage data from amplicon sequencing of a sample cohort as input. The method includes significance assessment, correction for multiple testing and does not depend on normal DNA controls. Budczies (2016 Mar 15) .
How to cite:
Jan Budczies (2015). ioncopy: Calling Copy Number Alterations in Amplicon Sequencing Data. R package version 2.2.2, https://cran.r-project.org/web/packages/ioncopy. Accessed 29 Oct. 2026.
Previous versions and publish date:
(2026-07-09 07:50), 1.0 (2015-08-26 14:53), 2.0.1 (2018-01-16 16:39), 2.0 (2017-12-05 22:39), 2.1.0 (2018-03-14 15:03), 2.1.1 (2018-03-23 23:04)
Other packages that cited ioncopy R package
View ioncopy citation profile
Other R packages that ioncopy depends, imports, suggests or enhances
Complete documentation for ioncopy
Functions, R codes and Examples using the ioncopy R package
Some associated functions: assess.CNA . calculate.CN . call.CNA . coverage . heatmap.CNA . ioncopy-package . read.coverages . runIoncopy . summarize.CNA . 
Some associated R codes: assess.CNA.R . calculate.CN.R . call.CNA.R . heatmap.CNA.R . read.coverages.R . runIoncopy.R . summarize.CNA.R .  Full ioncopy package functions and examples
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