Calling Copy Number Alterations in Amplicon Sequencing Data
Significance assessment of copy number alterations
Calculation of copy numbers
Gene-wise or amplicon-wise calling of copy number alterations
Visualization of Copy Number and CNA Calls
Calling copy number alterations in amplicon sequencing data
Helper function to read coverages from file system
Shiny app for Ioncopy
Summary of CNA calls
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) <doi:10.18632/oncotarget.7451>.