The generated wealth of immune repertoire sequencing data requires software to investigate and quantify inter- and intra-antibody repertoire evolution to uncover how B cells evolve during immune responses. Here, we present 'AntibodyForests', a software to investigate and quantify inter- and intra-antibody repertoire evolution.
| Version: | 1.0.0 |
| Depends: | R (≥ 4.0.0) |
| Imports: | ape, Biostrings, dplyr, graphics, grDevices, gtools, igraph, magrittr, parallel, pwalign, rlang, scales, seqinr, stats, stringdist, stringr, tidyr, utils, viridis |
| Suggests: | alakazam, base64enc, bio3d, combinat, devtools, DT, fpc, ggplot2, ggrepel, ggsignif, htmltools, knitr, msa, phangorn, pheatmap, Peptides, Rcompadre, rmarkdown, RPANDA, swipeR |
| Published: | 2025-01-23 |
| DOI: | 10.32614/CRAN.package.AntibodyForests |
| Author: | Daphne van Ginneken [aut, cre], Alexander Yermanos [aut], Valentijn Tromp [aut], Tudor-Stefan Cotet [ctb] |
| Maintainer: | Daphne van Ginneken <daphne.v.ginneken at gmail.com> |
| License: | GPL-2 |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | AntibodyForests results |
| Reference manual: | AntibodyForests.pdf |
| Vignettes: |
AntibodyForests vignette: building and analyzing B-cell lineage trees from 10x sc-V(D)J seq data (source, R code) |
| Package source: | AntibodyForests_1.0.0.tar.gz |
| Windows binaries: | r-devel: AntibodyForests_1.0.0.zip, r-release: AntibodyForests_1.0.0.zip, r-oldrel: not available |
| macOS binaries: | r-devel (arm64): AntibodyForests_1.0.0.tgz, r-release (arm64): AntibodyForests_1.0.0.tgz, r-oldrel (arm64): not available, r-devel (x86_64): AntibodyForests_1.0.0.tgz, r-release (x86_64): not available, r-oldrel (x86_64): not available |
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