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.

AuthorDaniel Gadala-Maria [aut, cre], Jason Vander Heiden [ctb], Steven Kleinstein [aut, cph]
Date of publication2016-08-28 16:20:50
MaintainerDaniel Gadala-Maria <daniel.gadala-maria@yale.edu>
LicenseCC BY-NC-SA 4.0
Version0.2.8
http://tigger.readthedocs.io

View on CRAN

Functions

cleanSeqs Man page
findNovelAlleles Man page
findUnmutatedCalls Man page
genotype Man page
genotypeFasta Man page
germline_ighv Man page
getMutatedPositions Man page
getMutCount Man page
getPopularMutationCount Man page
inferGenotype Man page
insertPolymorphisms Man page
novel_df Man page
plotGenotype Man page
plotNovel Man page
readIgFasta Man page
reassignAlleles Man page
sample_db Man page
selectNovel Man page
sortAlleles Man page
tigger Man page
tigger-package Man page
updateAlleleNames Man page
writeFasta Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.