Package: SeqFeatR 0.3.1

Bettina Budeus

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>.

Authors:Bettina Budeus

SeqFeatR_0.3.1.tar.gz
SeqFeatR_0.3.1.tar.gz(r-4.5-noble)SeqFeatR_0.3.1.tar.gz(r-4.4-noble)
SeqFeatR_0.3.1.tgz(r-4.4-emscripten)SeqFeatR_0.3.1.tgz(r-4.3-emscripten)
SeqFeatR.pdf |SeqFeatR.html
SeqFeatR/json (API)
NEWS

# Install 'SeqFeatR' in R:
install.packages('SeqFeatR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

jagscpp

2.30 score 261 downloads 2 mentions 18 exports 69 dependencies

Last updated 6 years agofrom:fc9916d2d3. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 13 2024
R-4.5-linuxOKDec 13 2024

Exports:assocpairassocpairfeatassocpointassocpointhierarchicalassocpointpairassoctuplecomparewithancestralfoundereffectfindergetfreqsorPlotqvaluesrewritetupleSeqFeatR_GUIsmallmanhattantartanvisualizepairvisualizepairfeatvolcanoplot

Dependencies:abindapeaskpassBiocGenericsBiostringsbootcalibrateclicodacolorspacecpp11crayoncurldigestfansifarverfastmatchgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrigraphIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslphangornpillarpkgconfigplotrixplyrquadprogqvalueR2jagsR2WinBUGSR6RColorBrewerRcppreshape2rjagsrlangS4Vectorsscalesstringistringrsystcltk2tibbleUCSC.utilsutf8vctrsviridisLitewidgetToolswithrXVectorzlibbioc

SeqFeatR Tutorial

Rendered fromSeqFeatR_tutorial.Rnwusingutils::Sweaveon Dec 13 2024.

Last update: 2018-03-06
Started: 2015-02-10