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:
SeqKat_0.0.8.tar.gz
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SeqKat.pdf |SeqKat.html✨
SeqKat/json (API)
NEWS
| # Install 'SeqKat' in R: |
| install.packages('SeqKat', repos = c('https://pboutros.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 years agofrom:fe65fd98eb. Checks:1 OK, 11 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 07 2025 |
| R-4.5-win-x86_64 | WARNING | Mar 07 2025 |
| R-4.5-mac-x86_64 | WARNING | Mar 07 2025 |
| R-4.5-mac-aarch64 | WARNING | Mar 07 2025 |
| R-4.5-linux-x86_64 | WARNING | Mar 07 2025 |
| R-4.4-win-x86_64 | WARNING | Mar 07 2025 |
| R-4.4-mac-x86_64 | WARNING | Mar 07 2025 |
| R-4.4-mac-aarch64 | WARNING | Mar 07 2025 |
| R-4.4-linux-x86_64 | WARNING | Mar 07 2025 |
| R-4.3-win-x86_64 | WARNING | Mar 07 2025 |
| R-4.3-mac-x86_64 | WARNING | Mar 07 2025 |
| R-4.3-mac-aarch64 | WARNING | Mar 07 2025 |
Exports:combine.tablefinal.scoreget.contextget.exprobntcxget.nucleotide.chunk.countsget.pairget.tnget.toptnget.trinucleotide.countsseqkattest.kataegis
Dependencies:codetoolsdoParallelforeachiteratorsRcpp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Combine Table | combine.table |
| Final Score | final.score |
| Get Context | get.context |
| get.exprobntcx | get.exprobntcx |
| Get Nucleotide Chunk Counts | get.nucleotide.chunk.counts |
| Get Pair | get.pair |
| Get Trinucleotides | get.tn |
| Get Top Trinucleotides | get.toptn |
| Get Trinucleotide Counts | get.trinucleotide.counts |
| SeqKat | seqkat |
| Test Kataegis | test.kataegis |
