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:
ioncopy_2.2.2.tar.gz
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ioncopy_2.2.2.tgz(r-4.4-any)ioncopy_2.2.2.tgz(r-4.3-any)
ioncopy_2.2.2.tar.gz(r-4.5-noble)ioncopy_2.2.2.tar.gz(r-4.4-noble)
ioncopy_2.2.2.tgz(r-4.4-emscripten)ioncopy_2.2.2.tgz(r-4.3-emscripten)
ioncopy.pdf |ioncopy.html✨
ioncopy/json (API)
| # Install 'ioncopy' in R: |
| install.packages('ioncopy', repos = c('https://budczies.r-universe.dev', 'https://cloud.r-project.org')) |
- coverage - Coverage data of 154 amplicons in 184 breast carcinomas
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 4 years agofrom:466f696ef9. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 03 2024 |
| R-4.5-win | OK | Sep 03 2024 |
| R-4.5-linux | OK | Sep 03 2024 |
| R-4.4-win | OK | Sep 03 2024 |
| R-4.4-mac | OK | Sep 03 2024 |
| R-4.3-win | OK | Sep 03 2024 |
| R-4.3-mac | OK | Sep 03 2024 |
Exports:assess.CNAcalculate.CNcall.CNAheatmap.CNAread.coveragesrunIoncopysummarize.CNA
Dependencies:base64encbslibcachemclicommonmarkcrayondigestfastmapfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlifecyclemagrittrmemoisemimepromisesR6rappdirsRcpprlangsassshinysourcetoolswithrxtablezip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calling copy number alterations in amplicon sequencing data | ioncopy-package ioncopy |
| Significance assessment of copy number alterations | assess.CNA |
| Calculation of copy numbers | calculate.CN |
| Gene-wise or amplicon-wise calling of copy number alterations | call.CNA |
| Coverage data of 154 amplicons in 184 breast carcinomas | coverage |
| Visualization of Copy Number and CNA Calls | heatmap.CNA |
| Helper function to read coverages from file system | read.coverages |
| Shiny app for Ioncopy | runIoncopy |
| Summary of CNA calls | summarize.CNA |
