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: 0.0.8
Depends: R (≥ 2.15.1), foreach, doParallel
Imports: Rcpp (≥ 0.11.0)
LinkingTo: Rcpp
Suggests: testthat, doMC, rmarkdown, knitr
Published: 2020-03-11
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

Downloads:

Reference manual: SeqKat.pdf
Vignettes: SeqKat
Package source: SeqKat_0.0.8.tar.gz
Windows binaries: r-prerelease: SeqKat_0.0.8.zip, r-release: SeqKat_0.0.8.zip, r-oldrel: SeqKat_0.0.8.zip
macOS binaries: r-prerelease: SeqKat_0.0.8.tgz, r-release: SeqKat_0.0.8.tgz, r-oldrel: SeqKat_0.0.8.tgz
Old sources: SeqKat archive

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