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Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses, see Budeus (2016) <doi:10.1371/journal.pone.0146409>.
| Version: | 0.3.1 |
| Depends: | R (≥ 3.2.2), tcltk, tcltk2, Biostrings, plotrix |
| Imports: | plyr, phangorn, qvalue, widgetTools, calibrate, ggplot2, R2jags, coda, scales, ape |
| Suggests: | xtable |
| Published: | 2019-04-12 |
| DOI: | 10.32614/CRAN.package.SeqFeatR |
| Author: | Bettina Budeus |
| Maintainer: | Bettina Budeus <bettina.budeus at stud.uni-due.de> |
| License: | GPL (≥ 3) |
| NeedsCompilation: | no |
| Citation: | SeqFeatR citation info |
| Materials: | NEWS INSTALL |
| CRAN checks: | SeqFeatR results |
| Reference manual: | SeqFeatR.pdf |
| Vignettes: |
SeqFeatR Tutorial |
| Package source: | SeqFeatR_0.3.1.tar.gz |
| Windows binaries: | r-devel: SeqFeatR_0.3.1.zip, r-release: SeqFeatR_0.3.1.zip, r-oldrel: SeqFeatR_0.3.1.zip |
| macOS binaries: | r-release (arm64): SeqFeatR_0.3.1.tgz, r-oldrel (arm64): SeqFeatR_0.3.1.tgz, r-release (x86_64): SeqFeatR_0.3.1.tgz, r-oldrel (x86_64): SeqFeatR_0.3.1.tgz |
| Old sources: | SeqFeatR archive |
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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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