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.

Author
Bettina Budeus
Date of publication
2016-10-17 12:41:09
Maintainer
Bettina Budeus <bettina.budeus@stud.uni-due.de>
License
GPL (>= 3)
Version
0.2.4

View on CRAN

Man pages

assocpair
Finding pairs of alignment positions that jointly mutate
assocpairfeat
Finding pairs of sequence alignment positions associated with...
assocpoint
Searches for associations of single alignment positions with...
assocpointhierarchical
Searches for associations of single alignment positions with...
assocpointpair
Compare results of SeqFeatRs assocpoint with SeqFeatRs...
assoctuple
Searches for associations of a tuple of alignment positions...
comparewithancestral
Compares ancestral sequence with sequence alignment
foundereffectfinder
Tries to identify a founder effect in results from SeqFeatRs...
getfreqs
Get frequencies for amino acids/nucleotides in alignment...
orPlot
Visualize odds ratios and p-values from SeqFeatRs assocpoint
q-values
Calculate q-values from p-values
rewritetuple
Rewrite result from SeqFeatRs assoctuple
SeqFeatR_GUI
GUI for SeqFeatR
SeqFeatR-package
Associates point and tuple mutations with sequence features.
smallmanhattan
A small version of manhattan plot
tartan
Visualize association of mutation pairs and features from two...
visualizepair
Visualize pairs of alignment positions that jointly mutate
visualizepairfeat
Visualize pairs of sequence alignment positions associated...
volcanoplot
Create volcano plot

Files in this package

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