AntibodyForests: Delineating Inter- And Intra-Antibody Repertoire Evolution

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

Documentation:

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)

Downloads:

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-release (arm64): AntibodyForests_1.0.0.tgz, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

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