AIRRDb |
Example human immune repertoire data |
cleanSeqs |
Clean up nucleotide sequences |
findNovelAlleles |
Find novel alleles from repertoire sequencing data |
findUnmutatedCalls |
Determine which calls represent an unmutated allele |
generateEvidence |
Generate evidence |
genotypeFasta |
Return the nucleotide sequences of a genotype |
GermlineIGHV |
Human IGHV germlines |
getMutatedPositions |
Find the location of mutations in a sequence |
getMutCount |
Determine the mutation counts from allele calls |
getPopularMutationCount |
Find mutation counts for frequency sequences |
inferGenotype |
Infer a subject-specific genotype using a frequency method |
inferGenotypeBayesian |
Infer a subject-specific genotype using a Bayesian approach |
insertPolymorphisms |
Insert polymorphisms into a nucleotide sequence |
plotGenotype |
Show a colorful representation of a genotype |
plotNovel |
Visualize evidence of novel V alleles |
readIgFasta |
Read immunoglobulin sequences |
reassignAlleles |
Correct allele calls based on a personalized genotype |
SampleDb |
Example human immune repertoire data |
SampleGenotype |
Example genotype inferrence results |
SampleGermlineIGHV |
Example Human IGHV germlines |
SampleNovel |
Example novel allele detection results |
selectNovel |
Select rows containing novel alleles |
sortAlleles |
Sort allele names |
subsampleDb |
Subsample repertoire |
tigger |
tigger |
updateAlleleNames |
Update IGHV allele names |
writeFasta |
Write to a fasta file |