Infers Novel Immunoglobulin Alleles from Sequencing Data


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Documentation for package ‘tigger’ version 0.3.1

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tigger-package tigger
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
SampleNovel Example novel allele detection results
selectNovel Select rows containing novel alleles
sortAlleles Sort allele names
tigger tigger
updateAlleleNames Update IGHV allele names
writeFasta Write to a fasta file