Package: SeqFeatR
Type: Package
Title: A Tool to Associate FASTA Sequences and Features
Version: 0.3.3
Date: 2026-02-13
Authors@R: person(given = "Bettina", family = "Budeus", role = c("aut", "cre"), email = "bettina.budeus@stud.uni-due.de")
Depends: R(>= 3.2.2),tcltk,tcltk2,Biostrings, plotrix
Imports: plyr, phangorn, qvalue, widgetTools, calibrate, ggplot2,
        R2jags, coda, scales, ape
Suggests: xtable
Description: 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>.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2026-06-24 20:37:11 UTC; root
Author: Bettina Budeus [aut, cre]
Maintainer: Bettina Budeus <bettina.budeus@stud.uni-due.de>
Config/pak/sysreqs: libglpk-dev jags libicu-dev libxml2-dev tcl tk
        tk-dev tk-table zlib1g-dev
Repository: https://cranhaven.r-universe.dev
Date/Publication: 2026-06-24 02:02:00 UTC
RemoteUrl: https://github.com/cranhaven/cranhaven.r-universe.dev
RemoteRef: package/SeqFeatR
RemoteSha: a28466ebb1c32416bf3feb842e2975cd0c4cdb6b
RemoteSubdir: SeqFeatR