Introduction | Input | Pre-processing of the data | Running RAbHIT | Infer haplotype by anchor gene | Haplotype with J6 as anchor | Haplotype with D2-21 as anchor | Compare multiple haplotypes | Inferring double chromosome deletion by relative gene usage | Interactive Haplotype inference with double chromosome deletions | Haplotype inference deletion heatmap | Inferring D/J single chromosome deletion by V pooled approach | Contact | References
Package: rabhit 0.4.0
rabhit: Inference Tool for Antibody Haplotype
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>.
Authors:
rabhit_0.4.0.tar.gz
rabhit_0.4.0.zip(r-4.7-any)rabhit_0.4.0.zip(r-4.6-any)rabhit_0.4.0.zip(r-4.5-any)
rabhit_0.4.0.tgz(r-4.6-any)rabhit_0.4.0.tgz(r-4.5-any)
rabhit_0.4.0.tar.gz(r-4.7-any)rabhit_0.4.0.tar.gz(r-4.6-any)
rabhit_0.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rabhit/json (API)
| # Install 'rabhit' in R: |
| install.packages('rabhit', repos = c('https://ayeletperes.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ayeletperes/rabhit/issues
Datasets:
- GENE.loc - Human Gene order on the chromosome
- GERM - Human germlines
- HDGERM - Human IGHD germlines
- HJGERM - Human IGHJ germlines
- HVGERM - Human IGHV germlines
- KJGERM - Human IGKJ germlines
- KVGERM - Human IGKV germlines
- LJGERM - Human IGLJ germlines
- LVGERM - Human IGKV germlines
- samples_db - Example IGH human naive b-cell repertiore
- samplesHaplotype - Example haplotype inference results
Last updated from:fe09e29b30. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 235 | ||
| source / vignettes | OK | 286 | ||
| linux-release | OK | 220 | ||
| macos-release | OK | 170 | ||
| macos-oldrel | OK | 112 | ||
| windows-devel | OK | 161 | ||
| windows-release | OK | 149 | ||
| windows-oldrel | OK | 166 | ||
| wasm-release | OK | 170 |
Exports:convertToASCcreateFullHaplotypecreateHaplotypeTabledeletionHeatmapdeletionsByBinomdeletionsByVpooledgeneUsagehapDendohapHeatmapnonReliableVGenesplotDeletionsByBinomplotDeletionsByVpooledplotHaplotypereadHaplotypeDb
Dependencies:clicowplotcpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
