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>.

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Description file content

Package
SeqFeatR
Type
Package
Title
A Tool to Associate FASTA Sequences and Features
Version
0.3.1
Date
2019-10-04
Author
Bettina Budeus
Maintainer
Bettina Budeus
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) .
License
GPL (>= 3)
NeedsCompilation
no
Packaged
2019-04-12 07:20:10 UTC; bettina
Repository
CRAN
Date/Publication
2019-04-12 12:02:37 UTC

install.packages('SeqFeatR')

0.3.1

3 months ago

Bettina Budeus

GPL (>= 3)

Depends on

R(>= 3.2.2),tcltk,tcltk2,Biostrings, plotrix

Imports

plyr, phangorn, qvalue, widgetTools, calibrate, ggplot2, R2jags, coda, scales, ape

Suggests

xtable

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