# R Tools for Inferring New Immunoglobulin Alleles from Rep-Seq Data

## Documentation for package ‘tigger’ version 0.2.8

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

## Help Pages

tigger-package | tigger
cleanSeqs | Clean up nucleotide sequences
findNovelAlleles | Find novel alleles from repertoire sequencing data
findUnmutatedCalls | Determine which calls represent an unmutated allele
genotype | Example of an Inferred Genotype
genotypeFasta | Return the nucleotide sequences of a genotype
germline_ighv | Human IGHV germlines
getMutatedPositions | Find the location of mutations in a sequence
getMutCount | Determine the mutation counts from allele calls
getPopularMutationCount | Find Frequent Sequences' Mutation Counts
inferGenotype | Infer a subject-specific genotype
insertPolymorphisms | Insert polymorphisms into a nucleotide sequence
novel_df | Example of Analyzed Rep-Seq data
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
sample_db | Example human Rep-Seq data
selectNovel | Select rows containing novel alleles
sortAlleles | Sort allele names
tigger | tigger
updateAlleleNames | Update IGHV allele names
writeFasta | Write to a fasta file