rabhit: Inference Tool for Antibody Haplotype

Infers V-D-J haplotypes and gene deletions from AIRR-seq data, based on IGHJ, IGHD or IGHV 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: 0.1.4
Depends: R (≥ 3.5.0), ggplot2 (≥ 2.0.0)
Imports: dplyr (≥ 0.5.0), reshape2 (≥ 1.4.3), plotly (≥ 4.7.1), graphics (≥ 3.4.4), gtools (≥ 3.5.0), cowplot (≥ 0.9.1), stats (≥ 3.4.4), dendextend (≥ 1.9.0), data.table (≥ 1.12.2), ggdendro (≥ 0.1.20), gridExtra (≥ 2.3.0), alakazam (≥ 0.2.10), tigger (≥ 0.2.11), methods (≥ 3.4.4), htmlwidgets (≥ 1.3.0), gtable (≥ 0.3.0), rlang (≥ 0.4.0), RColorBrewer (≥ 1.1.2), tidyr (≥ 0.8.3), stringi (≥ 1.4.3), grid (≥ 3.4.4), splitstackshape (≥ 1.4.8), fastmatch (≥ 1.1.0) , grDevices
Suggests: knitr, rmarkdown
Published: 2020-01-29
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/haplotyper/issues
License: CC BY-SA 4.0
URL: https://yaarilab.bitbucket.io/RAbHIT/
NeedsCompilation: no
Materials: README NEWS
CRAN checks: rabhit results

Downloads:

Reference manual: rabhit.pdf
Vignettes: Haplotype and deletion inference from B-cell repertoire
Package source: rabhit_0.1.4.tar.gz
Windows binaries: r-devel: rabhit_0.1.4.zip, r-release: rabhit_0.1.4.zip, r-oldrel: rabhit_0.1.4.zip
macOS binaries: r-release: rabhit_0.1.4.tgz, r-oldrel: rabhit_0.1.4.tgz
Old sources: rabhit archive

Linking:

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