Package: AntibodyForests 1.0.0

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_1.0.0.tar.gz
AntibodyForests_1.0.0.tar.gz(r-4.5-noble)AntibodyForests_1.0.0.tar.gz(r-4.4-noble)
AntibodyForests_1.0.0.tgz(r-4.4-emscripten)
AntibodyForests.pdf |AntibodyForests.html✨
AntibodyForests/json (API)

# Install 'AntibodyForests' in R:
install.packages('AntibodyForests', repos = 'https://cloud.r-project.org')
Datasets:
  • PLM_dataframe - Small PLM dataframe for function testing purposes
  • 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
  • small_af - Small AntibodyForests object for function testing purposes
  • small_vdj - Small VDJ dataframe for function testing purposes

On CRAN:

Conda:

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

2.70 score 262 downloads 23 exports 67 dependencies

Last updated 2 months agofrom:54922864ca. Checks:2 OK, 1 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 24 2025
R-4.5-linuxNOTEFeb 22 2025
R-4.4-linuxOKMar 24 2025

Exports:Af_add_node_featureAf_buildAf_cluster_metricsAf_cluster_node_featuresAf_compare_across_repertoiresAf_compare_methodsAf_compare_within_repertoiresAf_distance_boxplotAf_distance_scatterplotAf_edge_RMSDAf_get_sequencesAf_metricsAf_PLM_dataframeAf_plot_PLMAf_plot_treeAf_sync_nodesAf_to_newickcalculate_GBLDigraph_to_phyloVDJ_3d_propertiesVDJ_import_IgBLAST_annotationsVDJ_integrate_bulkVDJ_to_AIRR

Dependencies:ade4apeaskpassBiocGenericsBiostringsclicolorspacecpp11crayoncurldigestdplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegridExtragtablegtoolshttrigraphIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpixmappkgconfigpurrrpwalignR6RColorBrewerRcppRcppArmadillorlangS4VectorsscalessegmentedseqinrspstringdiststringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisviridisLitewithrXVector

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

Rendered fromAntibodyForests_vignette.Rmdusingknitr::rmarkdownon Mar 24 2025.

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

Citation

To cite package ‘AntibodyForests’ in publications use:

van Ginneken D, Yermanos A, Tromp V (2025). AntibodyForests: Delineating Inter- And Intra-Antibody Repertoire Evolution. R package version 1.0.0, https://CRAN.R-project.org/package=AntibodyForests.

Corresponding BibTeX entry: 

  @Manual{,
    title = {AntibodyForests: Delineating Inter- And Intra-Antibody
      Repertoire Evolution},
    author = {Daphne {van Ginneken} and Alexander Yermanos and
      Valentijn Tromp},
    year = {2025},
    note = {R package version 1.0.0},
    url = {https://CRAN.R-project.org/package=AntibodyForests},
  }

Readme and manuals

Delineating inter- and intra-antibody repertoire evolution with AntibodyForests

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.

This R package is currently composed of a pipeline to reconstruct lineage trees from 10x single-cell V(D)J sequencing data preprocessed with the Platypus package and compare trees within and across repertoires. Furthermore, it has modalities to integrate bulk RNA sequencing data, features of protein 3D structure, and evolutionary likelihoods generated with protein language models.

Installation

...

Help Manual

Help pageTopics
Function to add node features to an AntibodyForests-objectAf_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 clonotypesAf_cluster_metrics
Function to create a barplot of the cluster composition of selected features from each tree in an AntibodyForests-objectAf_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 tree topology of B cell lineagesAf_compare_within_repertoires
Small AntibodyForests object with default algorithm for function testing purposesaf_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-objectAf_distance_scatterplot
Function to calculate the RMSD between sequences over each edge in the AntibodyForest objectAf_edge_RMSD
Function to get the sequences from the nodes in an AntibodyForest objectAf_get_sequences
Function to calculate metrics for each tree in an AntibodyForests-objectAf_metrics
Small AntibodyForests object with MST algorithm for function testing purposesaf_mst
Small AntibodyForests object with NJ algorithm for function testing purposesaf_nj
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
Plots lineage tree of clonotype from AntibodyForests objectAf_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 fileAf_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/s13015-024-00267-1calculate_GBLD
Example output from Af_compare_within_repertoires() for function testing purposescompare_repertoire
Converts an igraph network into a phylogenetic tree as a phylo object.igraph_to_phylo
Small PLM dataframe for function testing purposesPLM_dataframe
Small AntibodyForests object for function testing purposessmall_af
Small VDJ dataframe for function testing purposessmall_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-objectVDJ_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 dataVDJ_integrate_bulk
Function to convert VDJ dataframe into an AIRR-formatted TSV file.VDJ_to_AIRR