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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
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

Documentation:

Reference manual: SeqKat.pdf
Vignettes: SeqKat

Downloads:

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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=SeqKat to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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