rabhit: Inference Tool for Antibody Haplotype

Infers V-D-J (Variable-Diversity-Joining) haplotypes and gene deletions from AIRR-seq (Adaptive Immune Receptor Repertoire sequencing) data for Ig (Immunoglobulin) and TR (T cell Receptor) chains, based on J (Joining), D (Diversity), or V (Variable) genes as anchor, by adapting a Bayesian framework. It also calculates a Bayes factor, a number that indicates the certainty level of the inference, for each haplotyped gene. Citation: Gidoni, et al (2019) <doi:10.1038/s41467-019-08489-3>. Peres and Gidoni, et al (2019) <doi:10.1093/bioinformatics/btz481>.

Version:	0.4.0
Depends:	R (≥ 3.5.0)
Imports:	ggplot2 (≥ 3.2.0), dplyr (≥ 1.0.0), tidyr (≥ 1.0.0), cowplot (≥ 0.9.1), gtable (≥ 0.3.0), grid, stats, utils, graphics, grDevices
Suggests:	knitr, rmarkdown, plotly (≥ 4.7.1), htmlwidgets (≥ 1.3.0), ggdendro (≥ 0.1.20), piglet, testthat (≥ 3.0.0)
Published:	2026-07-24
DOI:	10.32614/CRAN.package.rabhit
Author:	Ayelet Peres [aut, cre], Moriah Gidoni [aut], Gur Yaari [aut, cph]
Maintainer:	Ayelet Peres <ayelet.peres at yale.edu>
BugReports:	https://github.com/ayeletperes/rabhit/issues
License:	CC BY-SA 4.0
URL:	https://github.com/ayeletperes/rabhit, https://ayeletperes.github.io/rabhit/
NeedsCompilation:	no
Citation:	rabhit citation info
Materials:	README, NEWS
CRAN checks:	rabhit results

Documentation:

Reference manual:	rabhit.html , rabhit.pdf
Vignettes:	Haplotype and deletion inference from B-cell repertoire (source, R code)

Downloads:

Package source:	rabhit_0.4.0.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available
Old sources:	rabhit archive

Linking:

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