SeqKat: Detection of Kataegis
Kataegis is a localized hypermutation occurring when a region is enriched in somatic SNVs. Kataegis can result from multiple cytosine deaminations catalyzed by the AID/APOBEC family of proteins. This package contains functions to detect kataegis from SNVs in BED format. This package reports two scores per kataegic event, a hypermutation score and an APOBEC mediated kataegic score. Yousif, F. et al.; The Origins and Consequences of Localized and Global Somatic Hypermutation; Biorxiv 2018 <doi:10.1101/287839>.
| Version: |
0.0.9 |
| Depends: |
R (≥ 2.15.1), foreach, doParallel |
| Imports: |
Rcpp (≥ 0.11.0) |
| LinkingTo: |
Rcpp |
| Suggests: |
testthat, doMC, rmarkdown, knitr |
| Published: |
2026-01-24 |
| DOI: |
10.32614/CRAN.package.SeqKat |
| Author: |
Fouad Yousif [aut],
Xihui Lin [aut],
Fan Fan [aut],
Christopher Lalansingh [aut],
John Macdonald [aut],
Paul C. Boutros [cre] |
| Maintainer: |
Paul C. Boutros <pboutros at sbpdiscovery.org> |
| BugReports: |
https://github.com/TheBoutrosLab/package-SeqKat/issues |
| License: |
GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: |
https://github.com/TheBoutrosLab/package-SeqKat |
| NeedsCompilation: |
yes |
| Materials: |
README, NEWS |
| CRAN checks: |
SeqKat results |
Documentation:
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