Infers V-D-J haplotypes and gene deletions from AIRR-seq data for Ig and TR chains, based on J, D, or V 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: | 0.2.1 |
| Depends: | R (≥ 3.5.0), ggplot2 (≥ 3.2.0) |
| Imports: | dplyr (≥ 1.0.0), reshape2 (≥ 1.4.3), plotly (≥ 4.7.1), graphics (≥ 3.4.4), gtools (≥ 3.5.0), cowplot (≥ 0.9.1), readr (≥ 2.1.1), stats (≥ 4.1.0), dendextend (≥ 1.9.0), data.table (≥ 1.12.2), plyr (≥ 1.8.5), ggdendro (≥ 0.1.20), gridExtra (≥ 2.3.0), alakazam (≥ 1.0.0), tigger (≥ 1.0.0), methods (≥ 3.4.4), htmlwidgets (≥ 1.3.0), gtable (≥ 0.3.0), rlang (≥ 0.4.0), RColorBrewer (≥ 1.1.2), tidyr (≥ 1.0.0), stringi (≥ 1.4.3), grid (≥ 3.4.4), splitstackshape (≥ 1.4.8), fastmatch (≥ 1.1.0) , grDevices |
| Suggests: | knitr, rmarkdown |
| Published: | 2022-02-16 |
| Author: | Ayelet Peres [aut, cre], Moriah Gidoni [aut], Gur Yaari [aut, cph] |
| Maintainer: | Ayelet Peres <peresay at biu.ac.il> |
| BugReports: | https://bitbucket.org/yaarilab/rabhit/issues |
| License: | CC BY-SA 4.0 |
| URL: | https://yaarilab.bitbucket.io/RAbHIT/ |
| NeedsCompilation: | no |
| Materials: | README NEWS |
| CRAN checks: | rabhit results |
| Reference manual: | rabhit.pdf |
| Vignettes: |
Haplotype and deletion inference from B-cell repertoire |
| Package source: | rabhit_0.2.1.tar.gz |
| Windows binaries: | r-devel: rabhit_0.2.1.zip, r-release: rabhit_0.2.1.zip, r-oldrel: rabhit_0.2.1.zip |
| macOS binaries: | r-release (arm64): rabhit_0.2.1.tgz, r-oldrel (arm64): rabhit_0.2.1.tgz, r-release (x86_64): rabhit_0.2.1.tgz, r-oldrel (x86_64): rabhit_0.2.1.tgz |
| Old sources: | rabhit archive |
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