# Infers Novel Immunoglobulin Alleles from Sequencing Data

## Documentation for package ‘tigger’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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