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 |
| Reference manual: | rabhit.html , rabhit.pdf |
| Vignettes: |
Haplotype and deletion inference from B-cell repertoire (source, R code) |
| 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): rabhit_0.4.0.tgz, r-oldrel (arm64): rabhit_0.4.0.tgz, r-release (x86_64): rabhit_0.4.0.tgz, r-oldrel (x86_64): rabhit_0.4.0.tgz |
| Old sources: | rabhit archive |
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