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. SeqKat reports two scores per kataegic event, a hypermutation score and an APOBEC mediated kataegic score. Upon publication of the paper describing the methods used in this package, a reference will be added here.
| Version: | 0.0.4 |
| Depends: | R (≥ 2.15.1), foreach, doParallel |
| Imports: | Rcpp (≥ 0.11.0) |
| LinkingTo: | Rcpp |
| Suggests: | testthat, doMC, rmarkdown, knitr |
| Published: | 2017-06-25 |
| Author: | Fouad Yousif, Xihui Lin, Fan Fan, Christopher Lalansingh |
| Maintainer: | Paul C. Boutros <Paul.Boutros at oicr.on.ca> |
| License: | GPL-2 |
| NeedsCompilation: | yes |
| CRAN checks: | SeqKat results |
| Reference manual: | SeqKat.pdf |
| Vignettes: |
SeqKat |
| Package source: | SeqKat_0.0.4.tar.gz |
| Windows binaries: | r-devel: SeqKat_0.0.4.zip, r-release: SeqKat_0.0.4.zip, r-oldrel: SeqKat_0.0.4.zip |
| OS X El Capitan binaries: | r-release: SeqKat_0.0.4.tgz |
| OS X Mavericks binaries: | r-oldrel: SeqKat_0.0.4.tgz |
Please use the canonical form https://CRAN.R-project.org/package=SeqKat to link to this page.