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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: | 0.0.8 |
| Depends: | R (≥ 2.15.1), foreach, doParallel |
| Imports: | Rcpp (≥ 0.11.0) |
| LinkingTo: | Rcpp |
| Suggests: | testthat, doMC, rmarkdown, knitr |
| Published: | 2020-03-11 |
| DOI: | 10.32614/CRAN.package.SeqKat |
| Author: | Fouad Yousif, Xihui Lin, Fan Fan, Christopher Lalansingh, John Macdonald |
| Maintainer: | Paul C. Boutros <pboutros at mednet.ucla.edu> |
| License: | GPL-2 |
| NeedsCompilation: | yes |
| Materials: | NEWS |
| CRAN checks: | SeqKat results |
| Reference manual: | SeqKat.pdf |
| Vignettes: |
SeqKat |
| Package source: | SeqKat_0.0.8.tar.gz |
| Windows binaries: | r-devel: SeqKat_0.0.8.zip, r-release: SeqKat_0.0.8.zip, r-oldrel: SeqKat_0.0.8.zip |
| macOS binaries: | r-release (arm64): SeqKat_0.0.8.tgz, r-oldrel (arm64): SeqKat_0.0.8.tgz, r-release (x86_64): SeqKat_0.0.8.tgz, r-oldrel (x86_64): SeqKat_0.0.8.tgz |
| Old sources: | SeqKat archive |
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