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