R: A Tool to Associate FASTA Sequences and Features

# A Tool to Associate FASTA Sequences and Features

## Documentation for package ‘SeqFeatR’ version 0.3.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

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