{ "_id": "6a102845acfb0bcc41c9091f", "Package": "AntibodyForests", "Title": "Delineating Inter- And Intra-Antibody Repertoire Evolution", "Version": "1.1.0", "Authors@R": "c(\nperson(\"Daphne\", \"van Ginneken\", email = \"daphne.v.ginneken@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Alexander\", \"Yermanos\", role = \"aut\"),\nperson(\"Valentijn\", \"Tromp\", role = \"aut\"),\nperson(\"Tudor-Stefan\", \"Cotet\", role = \"ctb\")\n)", "Maintainer": "Daphne van Ginneken ", "Description": "The generated wealth of immune repertoire sequencing data\nrequires software to investigate and quantify inter- and\nintra-antibody repertoire evolution to uncover how B cells\nevolve during immune responses. Here, we present\n'AntibodyForests', a software to investigate and quantify\ninter- and intra-antibody repertoire evolution.", "License": "GPL-2", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-13 07:42:46 UTC", "User": "root" }, "Author": "Daphne van Ginneken [aut, cre], Alexander Yermanos [aut],\nValentijn Tromp [aut], Tudor-Stefan Cotet [ctb]", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2025-07-17 15:30:02 UTC", "RemoteUrl": "https://github.com/cran/AntibodyForests", "RemoteRef": "HEAD", "RemoteSha": "a1c1c44e65a321cc7e93e36820959faf9c16895a", "MD5sum": "1f3ee1bbcf9f92758c112763fc59b5d7", "_user": "cran", "_type": "src", "_file": "AntibodyForests_1.1.0.tar.gz", "_fileid": "62f30ce2536841da6991f99ca9d615f77aec3e6d9867c23aa59c30b01bb546b9", "_filesize": 2347266, "_sha256": "62f30ce2536841da6991f99ca9d615f77aec3e6d9867c23aa59c30b01bb546b9", "_created": "2026-05-13T07:42:46.000Z", "_published": "2026-05-22T09:56:21.033Z", "_distro": "noble", "_jobs": [ { "job": 77356822465, "time": 220, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6964377692" }, { "job": 77356822416, "time": 214, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6964375703" }, { "job": 77356822449, "time": 270, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6964309731" }, { "job": 77356822025, "time": 167, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7157771172" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/25785304536", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/AntibodyForests", "_commit": { "id": "a1c1c44e65a321cc7e93e36820959faf9c16895a", "author": "Daphne van Ginneken ", "committer": "cran-robot ", "message": "version 1.1.0\n", "time": 1752766202 }, "_maintainer": { "name": "Daphne van Ginneken", "email": "daphne.v.ginneken@gmail.com" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "ape", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "gtools", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "pwalign", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "seqinr", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringdist", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "alakazam", "role": "Suggests" }, { "package": "base64enc", "role": "Suggests" }, { "package": "bio3d", "role": "Suggests" }, { "package": "combinat", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "fpc", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "ggrepel", "role": "Suggests" }, { "package": "ggsignif", "role": "Suggests" }, { "package": "htmltools", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "msa", "role": "Suggests" }, { "package": "phangorn", "role": "Suggests" }, { "package": "pheatmap", "role": "Suggests" }, { "package": "philentropy", "role": "Suggests" }, { "package": "Peptides", "role": "Suggests" }, { "package": "Rcompadre", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "RPANDA", "role": "Suggests" }, { "package": "swipeR", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-29", "n": 1 } ], "_tags": [ { "name": "1.1.0", "date": "2025-07-17" } ], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 196, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/AntibodyForests" }, "_searchresults": 15, "_rbuild": "4.6.0", "_assets": [ "extra/AntibodyForests.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2025-01-23" }, { "version": "1.1.0", "date": "2025-07-17" } ], "_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" ], "_datasets": [ { "name": "af_default", "title": "Small AntibodyForests object with default algorithm for function testing purposes", "object": "af_default", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "af_mst", "title": "Small AntibodyForests object with MST algorithm for function testing purposes", "object": "af_mst", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "af_nj", "title": "Small AntibodyForests object with NJ algorithm for function testing purposes", "object": "af_nj", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "compare_repertoire", "title": "Example output from Af_compare_within_repertoires() for function testing purposes", "object": "compare_repertoire", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "PLM_dataframe", "title": "Small PLM dataframe for function testing purposes", "object": "PLM_dataframe", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sample", "clonotype", "n_subs", "node1", "node2", "mean_substitution_rank", "mean_substitution_probability", "mean_original_rank", "mean_original_probability", "mean_unmutating_rank", "mean_unmutating_probability" ], "rows": 60, "table": true, "tojson": true }, { "name": "small_af", "title": "Small AntibodyForests object for function testing purposes", "object": "small_af", "class": [ "AntibodyForests" ], "fields": [], "table": false, "tojson": false }, { "name": "small_vdj", "title": "Small VDJ dataframe for function testing purposes", "object": "small_vdj", "class": [ "data.frame" ], "fields": [ "sample_id", "barcode", "celltype", "isotype", "VDJ_contig_id", "VJ_contig_id", "VDJ_consensus_id", "VJ_consensus_id", "clonotype_id", "clonotype_frequency", "VDJ_chain", "VDJ_chain_count", "VDJ_umis", "VDJ_vgene", "VDJ_dgene", "VDJ_jgene", "VDJ_cgene", "VDJ_fwr1_nt", "VDJ_fwr1_aa", "VDJ_cdr1_nt", "VDJ_cdr1_aa", "VDJ_fwr2_nt", "VDJ_fwr2_aa", "VDJ_cdr2_nt", "VDJ_cdr2_aa", "VDJ_fwr3_nt", "VDJ_fwr3_aa", "VDJ_cdr3_nt", "VDJ_cdr3_aa", "VDJ_fwr4_nt", "VDJ_fwr4_aa", "VDJ_sequence_nt_raw", "VDJ_sequence_nt_trimmed", "VDJ_sequence_aa_trimmed", "VDJ_consensus_nt_raw", "VDJ_consensus_nt_trimmed", "VDJ_consensus_aa_trimmed", "VDJ_germline_nt_raw", "VDJ_germline_nt_trimmed", "VDJ_germline_aa_trimmed", "VJ_chain", "VJ_chain_count", "VJ_umis", "VJ_vgene", "VJ_jgene", "VJ_cgene", "VJ_fwr1_nt", "VJ_fwr1_aa", "VJ_cdr1_nt", "VJ_cdr1_aa", "VJ_fwr2_nt", "VJ_fwr2_aa", "VJ_cdr2_nt", "VJ_cdr2_aa", "VJ_fwr3_nt", "VJ_fwr3_aa", "VJ_cdr3_nt", "VJ_cdr3_aa", "VJ_fwr4_nt", "VJ_fwr4_aa", "VJ_sequence_nt_raw", "VJ_sequence_nt_trimmed", "VJ_sequence_aa_trimmed", "VJ_consensus_nt_raw", "VJ_consensus_nt_trimmed", "VJ_consensus_aa_trimmed", "VJ_germline_nt_raw", "VJ_germline_nt_trimmed", "VJ_germline_aa_trimmed", "SHM_count" ], "rows": 3671, "table": true, "tojson": true } ], "_help": [ { "page": "Af_add_node_feature", "title": "Function to add node features to an AntibodyForests-object", "topics": [ "Af_add_node_feature" ] }, { "page": "Af_build", "title": "Function to infer B cell evolutionary networks for all clonotypes in VDJ dataframe as obtained from the 'VDJ_build()' function.", "topics": [ "Af_build" ] }, { "page": "Af_cluster_metrics", "title": "Function to make a grouped boxplot of metrics from clusters of clonotypes", "topics": [ "Af_cluster_metrics" ] }, { "page": "Af_cluster_node_features", "title": "Function to create a barplot of the cluster composition of selected features from each tree in an AntibodyForests-object", "topics": [ "Af_cluster_node_features" ] }, { "page": "Af_compare_across_repertoires", "title": "A function to compare dynamics of B cell evolution across different repertoires.", "topics": [ "Af_compare_across_repertoires" ] }, { "page": "Af_compare_methods", "title": "Function to compare trees created with different algorithms from the same clonotype.", "topics": [ "Af_compare_methods" ] }, { "page": "Af_compare_PLM", "title": "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.", "topics": [ "Af_compare_PLM" ] }, { "page": "Af_compare_within_repertoires", "title": "Function to compare tree topology of B cell lineages", "topics": [ "Af_compare_within_repertoires" ] }, { "page": "af_default", "title": "Small AntibodyForests object with default algorithm for function testing purposes", "topics": [ "af_default" ] }, { "page": "Af_distance_boxplot", "title": "Function to make a grouped boxplot of distance between nodes from specific groups and the germline of lineage trees constructed with AntibodyForests.", "topics": [ "Af_distance_boxplot" ] }, { "page": "Af_distance_scatterplot", "title": "Function to scatterplot the distance to the germline to a numerical node feature of the AntibodyForests-object", "topics": [ "Af_distance_scatterplot" ] }, { "page": "Af_edge_RMSD", "title": "Function to calculate the RMSD between sequences over each edge in the AntibodyForest object", "topics": [ "Af_edge_RMSD" ] }, { "page": "Af_get_sequences", "title": "Function to get the sequences from the nodes in an AntibodyForest object", "topics": [ "Af_get_sequences" ] }, { "page": "Af_metrics", "title": "Function to calculate metrics for each tree in an AntibodyForests-object", "topics": [ "Af_metrics" ] }, { "page": "af_mst", "title": "Small AntibodyForests object with MST algorithm for function testing purposes", "topics": [ "af_mst" ] }, { "page": "af_nj", "title": "Small AntibodyForests object with NJ algorithm for function testing purposes", "topics": [ "af_nj" ] }, { "page": "Af_node_size_boxplot", "title": "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.", "topics": [ "Af_node_size_boxplot" ] }, { "page": "Af_PLM_dataframe", "title": "Function to create a dataframe of the Protein Language Model probabilities and ranks of the mutations along the edges of B cell lineage trees.", "topics": [ "Af_PLM_dataframe" ] }, { "page": "Af_plot_PLM", "title": "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.", "topics": [ "Af_plot_PLM" ] }, { "page": "Af_plot_PLM_mut_vs_cons", "title": "Function to create a boxplot of the Protein Language Model probabilities", "topics": [ "Af_plot_PLM_mut_vs_cons" ] }, { "page": "Af_plot_tree", "title": "Plots lineage tree of clonotype from AntibodyForests object", "topics": [ "Af_plot_tree" ] }, { "page": "Af_sync_nodes", "title": "Function to synchronize the node labels/names of all clonotypes within all samples of two AntibodyForests objects.", "topics": [ "Af_sync_nodes" ] }, { "page": "Af_to_newick", "title": "Saves an AntibodyForests-object into a newick file", "topics": [ "Af_to_newick" ] }, { "page": "calculate_GBLD", "title": "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", "topics": [ "calculate_GBLD" ] }, { "page": "compare_repertoire", "title": "Example output from Af_compare_within_repertoires() for function testing purposes", "topics": [ "compare_repertoire" ] }, { "page": "igraph_to_phylo", "title": "Converts an igraph network into a phylogenetic tree as a phylo object.", "topics": [ "igraph_to_phylo" ] }, { "page": "newick_to_Af", "title": "Converts files with phylogenetic trees in newick format into an AntibodyForests object.", "topics": [ "newick_to_Af" ] }, { "page": "PLM_dataframe", "title": "Small PLM dataframe for function testing purposes", "topics": [ "PLM_dataframe" ] }, { "page": "small_af", "title": "Small AntibodyForests object for function testing purposes", "topics": [ "small_af" ] }, { "page": "small_vdj", "title": "Small VDJ dataframe for function testing purposes", "topics": [ "small_vdj" ] }, { "page": "VDJ_3d_properties", "title": "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", "topics": [ "VDJ_3d_properties" ] }, { "page": "VDJ_import_IgBLAST_annotations", "title": "Function to import the annotations and alignments from IgBLAST output into the VDJ dataframe.", "topics": [ "VDJ_import_IgBLAST_annotations" ] }, { "page": "VDJ_integrate_bulk", "title": "A function to integrate bulk and single cell data", "topics": [ "VDJ_integrate_bulk" ] }, { "page": "VDJ_to_AIRR", "title": "Function to convert VDJ dataframe into an AIRR-formatted TSV file.", "topics": [ "VDJ_to_AIRR" ] } ], "_readme": "https://github.com/cran/AntibodyForests/raw/HEAD/README.md", "_rundeps": [ "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" ], "_vignettes": [ { "source": "AntibodyForests_vignette.Rmd", "filename": "AntibodyForests_vignette.html", "title": "AntibodyForests vignette: building and analyzing B-cell lineage trees from 10x sc-V(D)J seq data", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Quick start", "1. Import 10x output into VDJ dataframe with the VDJ_build() function", "Summary", "Parameters", "Example", "2. Construct lineage trees in repertoire-wide manner with the Af_build() function", "Examples", "1. Default", "2. ML", "3. IgPhyML", "3. Visualize lineage trees with the Af_plot_tree() function", "Maximum Likelihood", "With internal nodes", "Without internal nodes", "4. Compare tree construction methods with the Af_compare_methods() function", "Summary", "Parameters", "Af_compare_methods()", "5. Quantify evolution within repertoires with the Af_compare_within_repertoires() function", "Af_metrics()", "Af_compare_within_repertoires()", "Af_cluster_metrics()", "Af_cluster_node_features()", "Af_distance_boxplot()", "1. Euclidean distance", "2. Laplacian Spectral Density", "6. Compare antibody lineage trees across repertoires with the Af_compare_across_repertoires() function", "Af_compare_across_repertoires()", "Boxplot", "7. Assessing evolutionary likelihood of somatic hypermutation with Protein Language Models (PLM)", "Af_PLM_dataframe()", "Af_plot_PLM()", "Example1", "Example2", "Substitution Rank", "8. Investigate the evolution of antibody 3D structure along the lineage trees", "VDJ_3d_properties()", "Binding residues Antibody-Antigen", "Full antibody", "i. Run IgPhyML on VDJ dataframe and import IgPhyML trees into AntibodyForests object", "j. Integrate bulk RNA-seq sequences", "Contributions" ], "created": "2025-01-23 19:00:12", "modified": "2025-07-17 15:30:02", "commits": 2 } ], "_score": 2.8750612633917, "_indexed": true, "_nocasepkg": "antibodyforests", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.0", "date": "2026-05-13T07:46:01.000Z", "distro": "noble", "commit": "a1c1c44e65a321cc7e93e36820959faf9c16895a", "fileid": "0f22fac1812c44ca470a254df720534c7376cfc1a16ef1a403b3afa5ccd2a4de", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25785304536" }, { "r": "4.6.0", "os": "linux", "version": "1.1.0", "date": "2026-05-13T07:45:56.000Z", "distro": "noble", "commit": "a1c1c44e65a321cc7e93e36820959faf9c16895a", "fileid": "4302bf0972cda883e107c9e85ca1980d8db2533c48c29bc64cd9bd5d4438a25b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25785304536" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.0", "date": "2026-05-22T09:56:05.000Z", "commit": "a1c1c44e65a321cc7e93e36820959faf9c16895a", "fileid": "2c9fc12fd7ef92688d67d8b549eb1d818052b6d199da90cd7eaf0e94ad02638e", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/25785304536" } ] }