Package: ioncopy 2.2.2

ioncopy: Calling Copy Number Alterations in Amplicon Sequencing Data

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>.

Authors:Jan Budczies, Eva Romanovsky

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# Install 'ioncopy' in R:
install.packages('ioncopy', repos = c('https://budczies.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • coverage - Coverage data of 154 amplicons in 184 breast carcinomas

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.95 score 3 stars 4 scripts 210 downloads 3 mentions 7 exports 31 dependencies

Last updated 5 years agofrom:466f696ef9. Checks:9 OK. Indexed: yes.

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Exports:assess.CNAcalculate.CNcall.CNAheatmap.CNAread.coveragesrunIoncopysummarize.CNA

Dependencies:base64encbslibcachemclicommonmarkcrayondigestfastmapfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlifecyclemagrittrmemoisemimepromisesR6rappdirsRcpprlangsassshinysourcetoolswithrxtablezip