SeqFeatR discovers feature - sequence associations | The core of SeqFeatR: Fisher's exact test | Graphical output | Input: sequences and features | Multiple comparison correction | Hints | Advanced Feature: Bayes Factor in SeqFeatR | Advanced Feature: Discovering associations between mutation tuples and features | Tartan plot: visual comparison of different associations of features and sequence position tuples
This package is considered a duplicate. The official version of this package is found at:https://cran.r-universe.dev/SeqFeatR
Package: SeqFeatR 0.3.3
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:
SeqFeatR_0.3.3.tar.gz
SeqFeatR_0.3.3.zip(r-4.7)SeqFeatR_0.3.3.zip(r-4.6)SeqFeatR_0.3.3.zip(r-4.5)
SeqFeatR_0.3.3.tgz(r-4.6-any)SeqFeatR_0.3.3.tgz(r-4.5-any)
SeqFeatR_0.3.3.tar.gz(r-4.7-any)SeqFeatR_0.3.3.tar.gz(r-4.6-any)
SeqFeatR_0.3.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SeqFeatR/json (API)
| # Install 'SeqFeatR' in R: |
| install.packages('SeqFeatR', repos = c('https://cranhaven.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cranhaven/cranhaven.r-universe.dev/issues
archivedpackagesr-universejagscpp
Last updated from:a28466ebb1 (on package/SeqFeatR). Checks:7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 235 | ||
| source / vignettes | OK | 283 | ||
| linux-release-x86_64 | NOTE | 295 | ||
| macos-release-arm64 | NOTE | 181 | ||
| macos-oldrel-arm64 | NOTE | 211 | ||
| windows-devel | NOTE | 183 | ||
| windows-release | NOTE | 183 | ||
| windows-oldrel | NOTE | 178 | ||
| wasm-release | OK | 159 |
Exports:assocpairassocpairfeatassocpointassocpointhierarchicalassocpointpairassoctuplecomparewithancestralfoundereffectfindergetfreqsorPlotqvaluesrewritetupleSeqFeatR_GUIsmallmanhattantartanvisualizepairvisualizepairfeatvolcanoplot
Dependencies:abindapeBiocGenericsBiostringsbootcalibrateclicodacpp11crayondigestfarverfastmatchgenericsggplot2gluegtableigraphIRangesisobandlabelinglatticelifecyclemagrittrMASSMatrixnlmephangornpkgconfigplotrixplyrquadprogqvalueR2jagsR2WinBUGSR6RColorBrewerRcppreshape2rjagsrlangS4VectorsS7scalesSeqinfostringistringrtcltk2vctrsviridisLitewidgetToolswithrXVector
