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

Peer review:

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

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

2.70 score 23 exports 67 dependencies

Last updated 5 hours agofrom:54922864ca. Checks:2 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 23 2025
R-4.5-linuxOKJan 23 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 Jan 23 2025.

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

Readme and manuals

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