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.

AuthorBettina Budeus
Date of publication2016-10-17 12:41:09
MaintainerBettina Budeus <bettina.budeus@stud.uni-due.de>
LicenseGPL (>= 3)
Version0.2.4

View on CRAN

Functions

assocpair Man page
assocpairfeat Man page
assocpoint Man page
assocpointhierarchical Man page
assocpointpair Man page
assoctuple Man page
comparewithancestral Man page
foundereffectfinder Man page
getfreqs Man page
orPlot Man page
qvalues Man page
rewritetuple Man page
SeqFeatR_GUI Man page
SeqFeatR-package Man page
smallmanhattan Man page
tartan Man page
visualizepair Man page
visualizepairfeat Man page
volcanoplot Man page

Files

SeqFeatR
SeqFeatR/inst
SeqFeatR/inst/CITATION
SeqFeatR/inst/extdata
SeqFeatR/inst/extdata/Example_reference_nt.fasta
SeqFeatR/inst/extdata/assocpairfeat_results.csv
SeqFeatR/inst/extdata/Example_model_for_bayes.txt
SeqFeatR/inst/extdata/Example_nt.fasta
SeqFeatR/inst/extdata/Example_epitopes_aa.csv
SeqFeatR/inst/extdata/Example_HLA_binding_motifs_nt.csv
SeqFeatR/inst/extdata/Example_aa.fasta
SeqFeatR/inst/extdata/Example_reference_aa.fasta
SeqFeatR/inst/extdata/tart_1.csv
SeqFeatR/inst/extdata/Example_tree.nh
SeqFeatR/inst/extdata/Example_Consensus_nt.fasta
SeqFeatR/inst/extdata/shared_mutations_result_for_tartan.csv
SeqFeatR/inst/extdata/Example_Consensus_aa.fasta
SeqFeatR/inst/extdata/config.cfg
SeqFeatR/inst/extdata/Example_epitopes_nt.csv
SeqFeatR/inst/extdata/Example_HLA_binding_motifs_aa.csv
SeqFeatR/inst/extdata/Example_aa_for_cwa.fasta
SeqFeatR/inst/extdata/assocpoint_results.csv
SeqFeatR/inst/extdata/assocpair_results.csv
SeqFeatR/inst/extdata/assoctuple_result.csv
SeqFeatR/inst/extdata/tart_2.csv
SeqFeatR/inst/extdata/assocpoint_results_nt.csv
SeqFeatR/inst/doc
SeqFeatR/inst/doc/SeqFeatR_tutorial.pdf
SeqFeatR/inst/doc/SeqFeatR_tutorial.Rnw
SeqFeatR/NAMESPACE
SeqFeatR/INSTALL
SeqFeatR/NEWS
SeqFeatR/R
SeqFeatR/R/orPlot.R SeqFeatR/R/visualizepair.R SeqFeatR/R/assocpoint.R SeqFeatR/R/assocpointpair.R SeqFeatR/R/assocpair.R SeqFeatR/R/rewritetuple.R SeqFeatR/R/assocpairfeat.R SeqFeatR/R/SeqFeatR_GUI.R SeqFeatR/R/foundereffectfinder.R SeqFeatR/R/volcanoplot.R SeqFeatR/R/visualizepairfeat.R SeqFeatR/R/smallmanhattan.R SeqFeatR/R/comparewithancestral.R SeqFeatR/R/tartan.R SeqFeatR/R/getfreqs.R SeqFeatR/R/q-values.R SeqFeatR/R/assoctuple.R SeqFeatR/R/assocpointhierarchical.R
SeqFeatR/vignettes
SeqFeatR/vignettes/log.pdf_tex
SeqFeatR/vignettes/phylo_ex.svg
SeqFeatR/vignettes/Example_HLA_position.png
SeqFeatR/vignettes/screenshotHLA.png
SeqFeatR/vignettes/phylo_ex.pdf_tex
SeqFeatR/vignettes/SeqFeatR_tutorial.Rnw
SeqFeatR/vignettes/phylo_ex.pdf
SeqFeatR/vignettes/tart.pdf
SeqFeatR/vignettes/log.pdf
SeqFeatR/vignettes/OR_new.pdf
SeqFeatR/vignettes/tart.pdf_tex
SeqFeatR/vignettes/OR_new.pdf_tex
SeqFeatR/MD5
SeqFeatR/build
SeqFeatR/build/vignette.rds
SeqFeatR/DESCRIPTION
SeqFeatR/man
SeqFeatR/man/foundereffectfinder.Rd SeqFeatR/man/q-values.Rd SeqFeatR/man/rewritetuple.Rd SeqFeatR/man/volcanoplot.Rd SeqFeatR/man/assoctuple.Rd SeqFeatR/man/orPlot.Rd SeqFeatR/man/assocpair.Rd SeqFeatR/man/SeqFeatR_GUI.Rd SeqFeatR/man/tartan.Rd SeqFeatR/man/SeqFeatR-package.Rd SeqFeatR/man/smallmanhattan.Rd SeqFeatR/man/comparewithancestral.Rd SeqFeatR/man/assocpairfeat.Rd SeqFeatR/man/getfreqs.Rd SeqFeatR/man/assocpointpair.Rd SeqFeatR/man/visualizepair.Rd SeqFeatR/man/visualizepairfeat.Rd SeqFeatR/man/assocpoint.Rd SeqFeatR/man/assocpointhierarchical.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.