|assess.CNA||Significance assessment of copy number alterations|
|calculate.CN||Calculation of copy numbers|
|call.CNA||Gene-wise or amplicon-wise calling of copy number alterations|
|coverage||Coverage data of 154 amplicons in 184 breast carcinomas|
|heatmap.CNA||Visualization of Copy Number and CNA Calls|
|ioncopy-package||Calling copy number alterations in amplicon sequencing data|
|read.coverages||Helper function to read coverages from file system|
|runIoncopy||Shiny app for Ioncopy|
|summarize.CNA||Summary of CNA calls|
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