SeqFeatR: A Tool to Associate FASTA Sequences and Features

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:

Reference manual:	SeqFeatR.pdf
Vignettes:	SeqFeatR Tutorial

Downloads:

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

Linking:

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