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

Infers the V genotype of an individual from immunoglobulin (Ig) repertoire-sequencing (Rep-Seq) data, including detection of any novel alleles. This information is then used to correct existing V allele calls from among the sample sequences.

Author
Daniel Gadala-Maria [aut, cre], Jason Vander Heiden [ctb], Steven Kleinstein [aut, cph]
Date of publication
2016-08-28 16:20:50
Maintainer
Daniel Gadala-Maria <daniel.gadala-maria@yale.edu>
License
CC BY-NC-SA 4.0
Version
0.2.8
URLs

View on CRAN

Man pages

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

Files in this package

tigger
tigger/inst
tigger/inst/staticdocs
tigger/inst/staticdocs/index.R
tigger/inst/CITATION
tigger/inst/doc
tigger/inst/doc/Tigger-Vignette.pdf
tigger/inst/doc/Tigger-Vignette.R
tigger/inst/doc/Tigger-Vignette.Rmd
tigger/inst/markr
tigger/inst/markr/build.R
tigger/NAMESPACE
tigger/NEWS.md
tigger/data
tigger/data/germline_ighv.rda
tigger/data/genotype.rda
tigger/data/novel_df.rda
tigger/data/sample_db.rda
tigger/R
tigger/R/data.R
tigger/R/functions.R
tigger/R/tigger.R
tigger/vignettes
tigger/vignettes/index.php
tigger/vignettes/Tigger-Vignette.Rmd
tigger/README.md
tigger/MD5
tigger/build
tigger/build/vignette.rds
tigger/DESCRIPTION
tigger/man
tigger/man/findNovelAlleles.Rd
tigger/man/cleanSeqs.Rd
tigger/man/getPopularMutationCount.Rd
tigger/man/reassignAlleles.Rd
tigger/man/writeFasta.Rd
tigger/man/germline_ighv.Rd
tigger/man/getMutatedPositions.Rd
tigger/man/selectNovel.Rd
tigger/man/novel_df.Rd
tigger/man/genotype.Rd
tigger/man/findUnmutatedCalls.Rd
tigger/man/getMutCount.Rd
tigger/man/insertPolymorphisms.Rd
tigger/man/tigger.Rd
tigger/man/readIgFasta.Rd
tigger/man/sortAlleles.Rd
tigger/man/plotNovel.Rd
tigger/man/updateAlleleNames.Rd
tigger/man/plotGenotype.Rd
tigger/man/genotypeFasta.Rd
tigger/man/sample_db.Rd
tigger/man/inferGenotype.Rd