tigger: R Tools for Inferring New Immunoglobulin Alleles from Rep-Seq Data
Version 0.2.9.999

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.

Browse man pages Browse package API and functions Browse package files

AuthorDaniel Gadala-Maria [aut, cre], Jason Vander Heiden [ctb], Steven Kleinstein [aut, cph]
Date of publication2017-05-16 10:19:26 UTC
MaintainerDaniel Gadala-Maria <daniel.gadala-maria@yale.edu>
LicenseCC BY-SA 4.0
Version0.2.9.999
URL http://tigger.readthedocs.io
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("tigger")

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

Functions

cleanSeqs Man page Source code
findLowerY Source code
findNovelAlleles Man page Source code
findUnmutatedCalls Man page Source code
genotype Man page
genotypeFasta Man page Source code
germline_ighv Man page
getMutCount Man page Source code
getMutatedPositions Man page Source code
getPopularMutationCount Man page Source code
inferGenotype Man page Source code
insertPolymorphisms Man page Source code
multiplot Source code
mutationRangeSubset Source code
novel_df Man page
plotGenotype Man page Source code
plotNovel Man page Source code
positionMutations Source code
readIgFasta Man page Source code
reassignAlleles Man page Source code
sample_db Man page
selectNovel Man page Source code
sortAlleles Man page Source code
superSubstring Source code
tigger Man page
tigger-package Man page
updateAlleleNames Man page Source code
writeFasta Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/Tigger-Vignette.pdf
inst/doc/Tigger-Vignette.R
inst/doc/Tigger-Vignette.Rmd
inst/markr
inst/markr/build.R
NAMESPACE
NEWS.md
data
data/germline_ighv.rda
data/genotype.rda
data/novel_df.rda
data/sample_db.rda
R
R/data.R
R/functions.R
R/tigger.R
vignettes
vignettes/index.php
vignettes/Tigger-Vignette.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/findNovelAlleles.Rd
man/cleanSeqs.Rd
man/getPopularMutationCount.Rd
man/reassignAlleles.Rd
man/writeFasta.Rd
man/germline_ighv.Rd
man/getMutatedPositions.Rd
man/selectNovel.Rd
man/novel_df.Rd
man/genotype.Rd
man/findUnmutatedCalls.Rd
man/getMutCount.Rd
man/insertPolymorphisms.Rd
man/tigger.Rd
man/readIgFasta.Rd
man/sortAlleles.Rd
man/plotNovel.Rd
man/updateAlleleNames.Rd
man/plotGenotype.Rd
man/genotypeFasta.Rd
man/sample_db.Rd
man/inferGenotype.Rd
tigger documentation built on May 29, 2017, 8:59 p.m.