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


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Documentation for package ‘tigger’ version 0.2.11

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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
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