Background | Approach | Input | Running SeqKat | Output | Example | References
Package: SeqKat 0.0.9
Paul C. Boutros
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_0.0.9.tar.gz
SeqKat_0.0.9.zip(r-4.7-x86_64)SeqKat_0.0.9.zip(r-4.6-x86_64)SeqKat_0.0.9.zip(r-4.5-x86_64)
SeqKat_0.0.9.tgz(r-4.6-x86_64)SeqKat_0.0.9.tgz(r-4.6-arm64)SeqKat_0.0.9.tgz(r-4.5-x86_64)SeqKat_0.0.9.tgz(r-4.5-arm64)
SeqKat_0.0.9.tar.gz(r-4.7-arm64)SeqKat_0.0.9.tar.gz(r-4.7-x86_64)SeqKat_0.0.9.tar.gz(r-4.6-arm64)SeqKat_0.0.9.tar.gz(r-4.6-x86_64)
SeqKat_0.0.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SeqKat/json (API)
| # Install 'SeqKat' in R: |
| install.packages('SeqKat', repos = c('https://theboutroslab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/theboutroslab/package-seqkat/issues
Last updated from:464ce23291. Checks:11 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | WARNING | 142 | ||
| linux-devel-x86_64 | WARNING | 134 | ||
| source / vignettes | OK | 194 | ||
| linux-release-arm64 | WARNING | 153 | ||
| linux-release-x86_64 | WARNING | 136 | ||
| macos-release-arm64 | WARNING | 220 | ||
| macos-release-x86_64 | WARNING | 467 | ||
| macos-oldrel-arm64 | WARNING | 143 | ||
| macos-oldrel-x86_64 | WARNING | 425 | ||
| windows-devel | WARNING | 156 | ||
| windows-release | WARNING | 147 | ||
| windows-oldrel | WARNING | 128 | ||
| wasm-release | OK | 126 |
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 |
