Package: AntibodyForests 1.1.0

Daphne van Ginneken

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.

Authors:Daphne van Ginneken [aut, cre], Alexander Yermanos [aut], Valentijn Tromp [aut], Tudor-Stefan Cotet [ctb]

AntibodyForests_1.1.0.tar.gz
AntibodyForests_1.1.0.tar.gz(r-4.7-any)AntibodyForests_1.1.0.tar.gz(r-4.6-any)
AntibodyForests_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
AntibodyForests/json (API)

# Install 'AntibodyForests' in R:

install.packages('AntibodyForests', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

af_default - Small AntibodyForests object with default algorithm for function testing purposes
af_mst - Small AntibodyForests object with MST algorithm for function testing purposes
af_nj - Small AntibodyForests object with NJ algorithm for function testing purposes
compare_repertoire - Example output from Af_compare_within_repertoires() for function testing purposes
PLM_dataframe - Small PLM dataframe for function testing purposes
small_af - Small AntibodyForests object for function testing purposes
small_vdj - Small VDJ dataframe for function testing purposes

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.88 score 15 scripts 282 downloads 27 exports 55 dependencies

Last updated from:a1c1c44e65. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	249
source / vignettes	OK	287
linux-release-x86_64	OK	248
wasm-release	OK	195

Exports:Af_add_node_feature Af_build Af_cluster_metrics Af_cluster_node_features Af_compare_across_repertoires Af_compare_methods Af_compare_PLM Af_compare_within_repertoires Af_distance_boxplot Af_distance_scatterplot Af_edge_RMSD Af_get_sequences Af_metrics Af_node_size_boxplot Af_PLM_dataframe Af_plot_PLM Af_plot_PLM_mut_vs_cons Af_plot_tree Af_sync_nodes Af_to_newick calculate_GBLD igraph_to_phylo newick_to_Af VDJ_3d_properties VDJ_import_IgBLAST_annotations VDJ_integrate_bulk VDJ_to_AIRR

Dependencies:ade4 ape BiocGenerics Biostrings cli cpp11 crayon digest dplyr farver generics ggplot2 glue gridExtra gtable gtools igraph IRanges isoband labeling lattice lifecycle magrittr MASS Matrix nlme pillar pixmap pkgconfig purrr pwalign R6 RColorBrewer Rcpp RcppArmadillo rlang S4Vectors S7 scales segmented Seqinfo seqinr sp stringdist stringi stringr tibble tidyr tidyselect utf8 vctrs viridis viridisLite withr XVector

AntibodyForests vignette: building and analyzing B-cell lineage trees from 10x sc-V(D)J seq data

Rendered fromAntibodyForests_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-07-17
Started: 2025-01-23

Help page	Topics
Function to add node features to an AntibodyForests-object	Af_add_node_feature
Function to infer B cell evolutionary networks for all clonotypes in VDJ dataframe as obtained from the 'VDJ_build()' function.	Af_build
Function to make a grouped boxplot of metrics from clusters of clonotypes	Af_cluster_metrics
Function to create a barplot of the cluster composition of selected features from each tree in an AntibodyForests-object	Af_cluster_node_features
A function to compare dynamics of B cell evolution across different repertoires.	Af_compare_across_repertoires
Function to compare trees created with different algorithms from the same clonotype.	Af_compare_methods
Function to compare the distributions of the Protein Language Model probabilities or ranks of the mutations along the edges of B cell lineage trees across repertoires using the Jensen-Shannon divergence.	Af_compare_PLM
Function to compare tree topology of B cell lineages	Af_compare_within_repertoires
Small AntibodyForests object with default algorithm for function testing purposes	af_default
Function to make a grouped boxplot of distance between nodes from specific groups and the germline of lineage trees constructed with AntibodyForests.	Af_distance_boxplot
Function to scatterplot the distance to the germline to a numerical node feature of the AntibodyForests-object	Af_distance_scatterplot
Function to calculate the RMSD between sequences over each edge in the AntibodyForest object	Af_edge_RMSD
Function to get the sequences from the nodes in an AntibodyForest object	Af_get_sequences
Function to calculate metrics for each tree in an AntibodyForests-object	Af_metrics
Small AntibodyForests object with MST algorithm for function testing purposes	af_mst
Small AntibodyForests object with NJ algorithm for function testing purposes	af_nj
Function to make a grouped boxplot of the normalized average node sizes (number of cells with the exact same sequence) from specific groups of lineage trees constructed with AntibodyForests.	Af_node_size_boxplot
Function to create a dataframe of the Protein Language Model probabilities and ranks of the mutations along the edges of B cell lineage trees.	Af_PLM_dataframe
Function to create a distribution plot of the Protein Language Model probabilities and ranks of the mutations along the edges of B cell lineage trees.	Af_plot_PLM
Function to create a boxplot of the Protein Language Model probabilities	Af_plot_PLM_mut_vs_cons
Plots lineage tree of clonotype from AntibodyForests object	Af_plot_tree
Function to synchronize the node labels/names of all clonotypes within all samples of two AntibodyForests objects.	Af_sync_nodes
Saves an AntibodyForests-object into a newick file	Af_to_newick
Calculate the GBLD distance between trees in an AntibodyForests object. Code is derived from https://github.com/tahiri-lab/ClonalTreeClustering/blob/main/src/Python/GBLD_Metric_Final.ipynb Farnia, M., Tahiri, N. New generalized metric based on branch length distance to compare B cell lineage trees. Algorithms Mol Biol 19, 22 (2024). https://doi.org/10.1186/s13015-024-00267-1	calculate_GBLD
Example output from Af_compare_within_repertoires() for function testing purposes	compare_repertoire
Converts an igraph network into a phylogenetic tree as a phylo object.	igraph_to_phylo
Converts files with phylogenetic trees in newick format into an AntibodyForests object.	newick_to_Af
Small PLM dataframe for function testing purposes	PLM_dataframe
Small AntibodyForests object for function testing purposes	small_af
Small VDJ dataframe for function testing purposes	small_vdj
Function to calculate 3D-structure propoperties such as the average charge and hydrophobicity, pKa shift, free energy, RMSD of PDB files and add them to an AntibodyForests-object	VDJ_3d_properties
Function to import the annotations and alignments from IgBLAST output into the VDJ dataframe.	VDJ_import_IgBLAST_annotations
A function to integrate bulk and single cell data	VDJ_integrate_bulk
Function to convert VDJ dataframe into an AIRR-formatted TSV file.	VDJ_to_AIRR

Package: AntibodyForests 1.1.0

AntibodyForests: Delineating Inter- And Intra-Antibody Repertoire Evolution

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