foundereffectfinder
(Package: SeqFeatR) :
Tries to identify a founder effect in results from SeqFeatRs assocpair
Takes the result of co-mutation analysis like SeqFeatRs assocpair function and adds a column with a note if the row is in the same branch.
● Data Source:
CranContrib
● Keywords:
● Alias: foundereffectfinder
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q-values
(Package: SeqFeatR) :
Calculate q-values from p-values
Calculates and adds a column of q-values to a list of given p-values.
● Data Source:
CranContrib
● Keywords:
● Alias: qvalues
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rewritetuple
(Package: SeqFeatR) :
Rewrite result from SeqFeatRs assoctuple
Function to reqrite output from SeqFeatRs assoctuple into an usable form for SeqFeatRs tartan.
● Data Source:
CranContrib
● Keywords:
● Alias: rewritetuple
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Creates a pdf output file with a volcano plot out of the results from SeqFeatRs assocpoint.
● Data Source:
CranContrib
● Keywords:
● Alias: volcanoplot
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assoctuple
(Package: SeqFeatR) :
Searches for associations of a tuple of alignment positions with feature(s)
Searches for associations of tuple of nucleotide or amino acid sequence alignment positions with feature(s).
● Data Source:
CranContrib
● Keywords:
● Alias: assoctuple
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orPlot
(Package: SeqFeatR) :
Visualize odds ratios and p-values from SeqFeatRs assocpoint
Creates odds ratio/p-value plots for every feature and sequence alignment position.
● Data Source:
CranContrib
● Keywords:
● Alias: orPlot
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assocpair
(Package: SeqFeatR) :
Finding pairs of alignment positions that jointly mutate
Determines pairs of sequence alignment positions that mutate in a correlated fashion with respect to a consensus sequence.
● Data Source:
CranContrib
● Keywords:
● Alias: assocpair
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A GUI for all program features of SeqFeatR
● Data Source:
CranContrib
● Keywords:
● Alias: SeqFeatR_GUI
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tartan
(Package: SeqFeatR) :
Visualize association of mutation pairs and features from two (comparable) analyses.
Combines the results of two of SeqFeatRs assocpair or assoctuple analyses in one plot.
● Data Source:
CranContrib
● Keywords:
● Alias: tartan
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SeqFeatR
(Package: SeqFeatR) :
Associates point and tuple mutations with sequence features.
Package includes functions to analyze sequence alignments in FASTA format with known HLA types or other features. In case of HLA as a feature, possible HLA epitopes are predicted based on clusters of HLA-associated mutations. Various plots are provided to visualize results.
● Data Source:
CranContrib
● Keywords: package
● Alias: SeqFeatR-package
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providing 
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