Package: SeqKat 0.0.8

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>.

Authors:Fouad Yousif, Xihui Lin, Fan Fan, Christopher Lalansingh, John Macdonald

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SeqKat/json (API)
NEWS

# Install 'SeqKat' in R:
install.packages('SeqKat', repos = c('https://pboutros.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.11 score 13 scripts 141 downloads 1 mentions 11 exports 5 dependencies

Last updated 5 years agofrom:fe65fd98eb. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 07 2024
R-4.5-win-x86_64WARNINGNov 07 2024
R-4.5-linux-x86_64WARNINGNov 07 2024
R-4.4-win-x86_64WARNINGNov 07 2024
R-4.4-mac-x86_64WARNINGNov 07 2024
R-4.4-mac-aarch64WARNINGNov 07 2024
R-4.3-win-x86_64WARNINGNov 07 2024
R-4.3-mac-x86_64WARNINGNov 07 2024
R-4.3-mac-aarch64WARNINGNov 07 2024

Exports:combine.tablefinal.scoreget.contextget.exprobntcxget.nucleotide.chunk.countsget.pairget.tnget.toptnget.trinucleotide.countsseqkattest.kataegis

Dependencies:codetoolsdoParallelforeachiteratorsRcpp

SeqKat

Rendered fromvignette.Rmdusingknitr::rmarkdownon Nov 07 2024.

Last update: 2018-03-29
Started: 2017-06-25

Readme and manuals

Help Manual

Help pageTopics
Combine Tablecombine.table
Final Scorefinal.score
Get Contextget.context
get.exprobntcxget.exprobntcx
Get Nucleotide Chunk Countsget.nucleotide.chunk.counts
Get Pairget.pair
Get Trinucleotidesget.tn
Get Top Trinucleotidesget.toptn
Get Trinucleotide Countsget.trinucleotide.counts
SeqKatseqkat
Test Kataegistest.kataegis