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ioncopy (version 2.2.2)

Calling Copy Number Alterations in Amplicon Sequencing Data

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) .

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Version

Install

install.packages('ioncopy')

Monthly Downloads

187

Version

2.2.2

License

GPL-3

Maintainer

Jan Budczies

Last Published

August 11th, 2020

Functions in ioncopy (2.2.2)

call.CNA

Gene-wise or amplicon-wise calling of copy number alterations
assess.CNA

Significance assessment of copy number alterations
heatmap.CNA

Visualization of Copy Number and CNA Calls
read.coverages

Helper function to read coverages from file system
summarize.CNA

Summary of CNA calls
runIoncopy

Shiny app for Ioncopy
ioncopy-package

Calling copy number alterations in amplicon sequencing data
coverage

Coverage data of 154 amplicons in 184 breast carcinomas
calculate.CN

Calculation of copy numbers