{ "_id": "6a265793794753ddbc3e4772", "Package": "dowser", "Type": "Package", "Version": "2.4.2", "Date": "2026-03-25", "Authors@R": "c(\nperson(\"Kenneth\", \"Hoehn\", email = \"kenneth.b.hoehn@dartmouth.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Cole\", \"Jensen\", email = \"cole.jensen@yale.edu\", role = \"aut\"),\nperson(\"Jessie\", \"Fielding\", email = \"jessie.jo.fielding@dartmouth.edu\", role = \"aut\"),\nperson(\"Hunter\", \"Melton\", email = \"hunter.j.melton@dartmouth.edu\", role = \"aut\"),\nperson(\"Susanna\", \"Marquez\", email = \"susanna.marquez@yale.edu\", role = \"ctb\"),\nperson(\"Jason\", \"Vander Heiden\", email = \"jason.vanderheiden@gmail.com\", role = \"ctb\"),\nperson(\"Erick\", \"Matsen\", role = \"ctb\"),\nperson(\"Steven\", \"Kleinstein\", email = \"steven.kleinstein@yale.edu\", role = c(\"aut\", \"cph\"))\n)", "Title": "B Cell Receptor Phylogenetics Toolkit", "Description": "Provides a set of functions for inferring, visualizing,\nand analyzing B cell phylogenetic trees. Provides methods to 1)\nreconstruct unmutated ancestral sequences, 2) build B cell\nphylogenetic trees using multiple methods, 3) visualize trees\nwith metadata at the tips, 4) reconstruct intermediate\nsequences, 5) detect biased ancestor-descendant relationships\namong metadata types Workflow examples available at\ndocumentation site (see URL). 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{ "page": "bootstrapTrees", "title": "Deprecated! Please use findSwitches instead.", "topics": [ "bootstrapTrees" ] }, { "page": "buildAllClonalGermlines", "title": "buildAllClonalGermlines Determines and builds all possible germlines for a clone", "topics": [ "buildAllClonalGermlines" ] }, { "page": "buildBeast", "title": "Read in a directory from a BEAST run. Runs treeannotator and loganalyser.", "topics": [ "buildBeast" ] }, { "page": "buildClonalGermline", "title": "'buildClonalGermline' Determine consensus clone sequence and create germline for clone", "topics": [ "buildClonalGermline" ] }, { "page": "buildGermline", "title": "'buildGermline' reconstruct germline segments from alignment data", "topics": [ "buildGermline" ] }, { "page": "buildIgphyml", "title": "Wrapper to build IgPhyML trees and infer intermediate nodes", "topics": [ "buildIgphyml" ] }, { "page": "buildPhylo", "title": "Wrapper for alakazam::buildPhylipLineage", "topics": [ "buildPhylo" ] }, { "page": "buildPML", "title": "Wrapper for phangorn::optim.pml", "topics": [ "buildPML" ] }, { "page": "buildPratchet", "title": "Wrapper for phangorn::pratchet", "topics": [ "buildPratchet" ] }, { "page": "buildRAxML", "title": "Wrapper to build RAxML-ng trees and infer intermediate nodes", "topics": [ "buildRAxML" ] }, { "page": "calcRF", "title": "Finds the Robinson-Fould's cluster distance between phylogenies.", "topics": [ "calcRF" ] }, { "page": "checkDivergence", "title": "Compare divergence along a tree in terms of mutations (sum of branches) for each tip and reconstructed internal node to its Hamming distance from the germline. Divergence should never be less than Hamming distance. A threshold of -1 is used to represent 1 full mutation difference. The function will throw a warning if any trees cross this threshold", "topics": [ "checkDivergence" ] }, { "page": "collapseNodes", "title": "Collapse internal nodes with the same predicted sequence", "topics": [ "collapseNodes" ] }, { "page": "colorTrees", "title": "Get a color palette for a predefined set of trait values", "topics": [ "colorTrees" ] }, { "page": "condenseTrees", "title": "Condense a set of equally parsimonious node labels into a single tree", "topics": [ "condenseTrees" ] }, { "page": "correlationTest", "title": "Run date randomization test for temporal signal on a set of trees.", "topics": [ "correlationTest" ] }, { "page": "create_alignment", "title": "Takes an airr clone object and returns BEAST2 Alignment xml of the sequences", "topics": [ "create_alignment" ] }, { "page": "create_height_prior", "title": "Takes an airr clone object and returns BEAST2 XML to set a height prior", "topics": [ "create_height_prior" ] }, { "page": "create_max_height_prior", "title": "Takes an airr clone object and returns BEAST2 XML to set a maximum height prior", "topics": [ "create_max_height_prior" ] }, { "page": "create_MRCA_prior_germline", "title": "Takes an airr clone object and returns BEAST2 XML for MRCA prior of the germline sequence", "topics": [ "create_MRCA_prior_germline" ] }, { "page": "create_MRCA_prior_observed", "title": "Takes an airr clone object and returns BEAST2 XML for MRCA prior of the observed sequences", "topics": [ "create_MRCA_prior_observed" ] }, { "page": "create_root_freqs", "title": "Takes an airr clone object and returns BEAST2 rootfreqs xml of the germline", "topics": [ "create_root_freqs" ] }, { "page": "create_starting_tree", "title": "Takes an airr clone object and tree and returns BEAST2 XML for setting the starting tree", "topics": [ "create_starting_tree" ] }, { "page": "create_traitset", "title": "Takes an airr clone object and returns BEAST2 XML for a trait/traitSet from a column", "topics": [ "create_traitset" ] }, { "page": "createAllGermlines", "title": "createAllGermlines Creates all possible germlines for a clone", "topics": [ "createAllGermlines" ] }, { "page": "createGermlines", "title": "createGermlines Determine consensus clone sequence and create germline for clone", "topics": [ "createGermlines" ] }, { "page": "dfToFasta", "title": "Write a fasta file of sequences 'readFasta' reads a fasta file", "topics": [ "dfToFasta" ] }, { "page": "downsampleClone", "title": "'downsampleClone' Down-sample clone to maximum tip/switch ratio", "topics": [ "downsampleClone" ] }, { "page": "dowser", "title": "The dowser package", "topics": [ "dowser" ] }, { "page": "ExampleAirr", "title": "Example AIRR database", "topics": [ "ExampleAirr" ] }, { "page": "ExampleAirrTyCHE", "title": "Example AIRR database for TyCHE", "topics": [ "ExampleAirrTyCHE" ] }, { "page": "ExampleClones", "title": "Example Ig lineage trees", "topics": [ "ExampleClones" ] }, { "page": "ExampleDbChangeo", "title": "Example Change-O database", "topics": [ "ExampleDbChangeo" ] }, { "page": "ExampleMixedClones", "title": "Example Multiple Partition Trees", "topics": [ "ExampleMixedClones" ] }, { "page": "ExampleMixedDb", "title": "Example Change-O database", "topics": [ "ExampleMixedDb" ] }, { "page": "exportTrees", "title": "Exports the phylogenetic trees from the airrClone object", "topics": [ "exportTrees" ] }, { "page": "filterPartialSeqs", "title": "'filterPartialSeqs'", "topics": [ "filterPartialSeqs" ] }, { "page": "findSwitches", "title": "Create a bootstrap distribution for clone sequence alignments, and estimate trees for each bootstrap replicate.", "topics": [ "findSwitches" ] }, { "page": "formatClones", "title": "Generate an ordered list of airrClone objects for lineage construction", "topics": [ "formatClones" ] }, { "page": "getAllSeqs", "title": "Return all tip and internal node sequences", "topics": [ "getAllSeqs" ] }, { "page": "getBootstraps", "title": "Creates a bootstrap distribution for clone sequence alignments, and returns estimated trees for each bootstrap replicate as a nested list as a new input tibble column.", "topics": [ "getBootstraps" ] }, { "page": "getDiffPoint", "title": "Recurse up to tree to find most recent node with different state, or the root", "topics": [ "getDiffPoint" ] }, { "page": "getDiffPoints", "title": "For each tree, recurse up to tree to find most recent node with a different state, or the root", "topics": [ "getDiffPoints" ] }, { "page": "getDivergence", "title": "Get divergence from root of tree for each tip", "topics": [ "getDivergence" ] }, { "page": "getGermline", "title": "getGermline get germline segment from specified receptor and segment", "topics": [ "getGermline" ] }, { "page": "getNodeSeq", "title": "Return IMGT gapped sequence of specified tree node", "topics": [ "getNodeSeq" ] }, { "page": "getPalette", "title": "Get a color palette for a predefined set of trait values. 'Germline' defaults to black unless specified.", "topics": [ "getPalette" ] }, { "page": "getSeq", "title": "Deprecated! Use getNodeSeq", "topics": [ "getSeq" ] }, { "page": "getSkylines", "title": "Make data frames for Bayesian skyline plots", "topics": [ "getSkylines" ] }, { "page": "getSubclones", "title": "#' Deprecated! Use resolveLightChains", "topics": [ "getSubclones" ] }, { "page": "getSubTaxa", "title": "Get the tip labels as part of a clade defined by an internal node", "topics": [ "getSubTaxa" ] }, { "page": "getTimeTrees", "title": "Estimate time trees by running BEAST on each clone Applies XML 'template' to each clone", "topics": [ "getTimeTrees" ] }, { "page": "getTimeTreesIterate", "title": "Iteratively resume getTimeTrees until convergence, as defined by all parameters (except those in 'ignore' vector) having ESS greater than or equal to the specified ess_cutoff", "topics": [ "getTimeTreesIterate" ] }, { "page": "getTrees", "title": "Estimate lineage tree topologies, branch lengths, and internal node states if desired", "topics": [ "getTrees" ] }, { "page": "getTreesAndUCAs", "title": "getTreesAndUCAs Construct trees and infer the UCA", "topics": [ "getTreesAndUCAs" ] }, { "page": "IsotypeTrees", "title": "Example Ig lineage trees with isotype reconstructions.", "topics": [ "IsotypeTrees" ] }, { "page": "makeAirrClone", "title": "Generate a airrClone object for lineage construction", "topics": [ "makeAirrClone" ] }, { "page": "makeModelFile", "title": "Make a parsimony model file", "topics": [ "makeModelFile" ] }, { "page": "makeSkyline", "title": "get values for Bayesian Skyline plot", "topics": [ "makeSkyline" ] }, { "page": "maskCodons", "title": "'maskCodons' Masks codons split by insertions", "topics": [ "maskCodons" ] }, { "page": "maskSequences", "title": "'maskSequences' Mask codons split by insertions in V gene", "topics": [ "maskSequences" ] }, { "page": "plotSkylines", "title": "Simple function for plotting Bayesian skyline plots", "topics": [ "plotSkylines" ] }, { "page": "plotTrees", "title": "Plot a tree with colored internal node labels using ggtree", "topics": [ "plotTrees" ] }, { "page": "readBEAST", "title": "Reads in a BEAST output directory", "topics": [ "readBEAST" ] }, { "page": "readFasta", "title": "Read a fasta file into a list of sequences 'readFasta' reads a fasta file", "topics": [ "readFasta" ] }, { "page": "readIMGT", "title": "'readIMGT' read in IMGT database", "topics": [ "readIMGT" ] }, { "page": "readLineages", "title": "Read in all trees from a lineages file", "topics": [ "readLineages" ] }, { "page": "readModelFile", "title": "Read in a parsimony model file", "topics": [ "readModelFile" ] }, { "page": "reconIgPhyML", "title": "Do IgPhyML maximum parsimony reconstruction", "topics": [ "reconIgPhyML" ] }, { "page": "rerootTree", "title": "Reroot phylogenetic tree to have its germline sequence at a zero-length branch to a node which is the direct ancestor of the tree's UCA. Assigns 'uca' to be the ancestral node to the tree's germline sequence, as 'germid' as the tree's germline sequence ID.", "topics": [ "rerootTree" ] }, { "page": "resolveLightChains", "title": "Define subgroups within clones based on light chain rearrangements", "topics": [ "resolveLightChains" ] }, { "page": "resolvePolytomies", "title": "Resolve polytomies to have the minimum number of single timepoint clades", "topics": [ "resolvePolytomies" ] }, { "page": "runCorrelationTest", "title": "Run correlationTest, based on https://doi.org/10.1111/2041-210X.12466", "topics": [ "runCorrelationTest" ] }, { "page": "sampleCloneMultiGroup", "title": "'sampleCloneMultiGroup' Down-sample clone to specified size with one or multiple groups to sample evenly", "topics": [ "sampleCloneMultiGroup" ] }, { "page": "sampleClones", "title": "'sampleClones' Down-sample clones to specified size", "topics": [ "sampleClones" ] }, { "page": "scaleBranches", "title": "Scale branch lengths to represent either mutations or mutations per site.", "topics": [ "scaleBranches" ] }, { "page": "stitchRegions", "title": "stitchRegions Similar to stitchVDJ but with segment IDs instead of nucleotides", "topics": [ "stitchRegions" ] }, { "page": "stitchVDJ", "title": "stitchVDJ combines germline gene segments to a single string", "topics": [ "stitchVDJ" ] }, { "page": "stopCodonCheck", "title": "Check whether sequences have in-frame premature stop codons (PTCs)", "topics": [ "stopCodonCheck" ] }, { "page": "testPS", "title": "Performs PS (parsimony score) test on switch data", "topics": [ "testPS" ] }, { "page": "testSC", "title": "Performs SC (switch count) test on switch data", "topics": [ "testSC" ] }, { "page": "testSP", "title": "Performs SP (switch proportion) test on switch data", "topics": [ "testSP" ] }, { "page": "TimeTrees", "title": "Example Ig lineage trees sampled over time.", "topics": [ "TimeTrees" ] }, { "page": "treesToPDF", "title": "Simple function for plotting a lot of trees into a pdf", "topics": [ "treesToPDF" ] }, { "page": "write_clone_to_xml", "title": "Takes an airr clone object and template and writes a BEAST2 XML file", "topics": [ "write_clone_to_xml" ] }, { "page": "write_clones_to_xmls", "title": "Wrapper to write multiple clones to XML files", "topics": [ "write_clones_to_xmls" ] }, { "page": "writeCloneSequences", "title": "Write the sequences used in tree building to a fasta format. If there are more than one tree in airrClone output the sequence id will be followed by \"|clone_id\".", "topics": [ "writeCloneSequences" ] }, { "page": "writeFasta", "title": "'writeFasta' Write a fasta file of sequences given a named list of sequences", "topics": [ "writeFasta" ] }, { "page": "writeLineageFile", "title": "Write lineage file for IgPhyML use", "topics": [ "writeLineageFile" ] } ], "_readme": "https://github.com/immcantation/dowser/raw/HEAD/README.md", "_rundeps": [ "abind", "ade4", "airr", "alakazam", "ape", "aplot", "base64enc", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "bslib", "cachem", "cigarillo", "cli", "clipr", "codetools", "commonmark", "cpp11", "crayon", "DelayedArray", "digest", "diptest", "doParallel", "dplyr", "evaluate", "farver", "fastmap", "fastmatch", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "foreach", "formatR", "fs", "futile.logger", "futile.options", "gdtools", "generics", "GenomicAlignments", "GenomicRanges", "ggfun", "ggiraph", "ggplot2", "ggplotify", "ggtree", "glue", "gridExtra", "gridGraphics", "gtable", "highr", "hms", "htmltools", "htmlwidgets", "igraph", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lambda.r", "lattice", "lazyeval", "lifecycle", "litedown", "magrittr", "markdown", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "nlme", "patchwork", "phangorn", "phylotate", "pillar", "pixmap", "pkgconfig", "prettyunits", "progress", "purrr", "pwalign", "quadprog", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "readr", "Rhtslib", "rlang", "rmarkdown", "Rsamtools", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "segmented", "Seqinfo", "seqinr", "shazam", "snow", "sp", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "systemfonts", "tibble", "tidyr", "tidyselect", "tidytree", "tinytex", "treeio", "tzdb", "utf8", "vctrs", "viridisLite", "vroom", "withr", "xfun", "XVector", "yaml", "yulab.utils" ], "_vignettes": [ { "source": "Building-Trees-Vignette.Rmd", "filename": "Building-Trees-Vignette.html", "title": "Build B cell lineage trees", "author": "Kenneth B. Hoehn", "engine": "knitr::rmarkdown", "headings": [ "Format clones", "Build maximum parsimony trees", "Build maximum likelihood trees", "Build IgPhyML B cell trees", "Building maximum likelihood trees with multiple partitions" ], "created": "2021-07-14 16:15:14", "modified": "2026-03-26 15:20:00", "commits": 21 }, { "source": "Building-Time-Trees-Vignette.Rmd", "filename": "Building-Time-Trees-Vignette.html", "title": "Build Time Trees Using TyCHE and BEAST", "author": "Jessie Fielding", "engine": "knitr::rmarkdown", "headings": [ "Building Time Trees", "Requirements", "For Mac and Windows machines, we recommend:", "For Linux machines, we recommend running:", "Download and set up XML templates", "Setting up data", "Estimating the GC clock rate", "Run getTimeTreesIterate with a TyCHE template", "Visualize the results" ], "created": "2025-10-13 20:41:21", "modified": "2026-01-06 20:39:24", "commits": 2 }, { "source": "Resolve-Light-Chains-Vignette.Rmd", "filename": "Resolve-Light-Chains-Vignette.html", "title": "Building trees with paired heavy and light chain data", "author": "Cole G. Jensen", "engine": "knitr::rmarkdown", "headings": [ "Resolve light chains", "Reconstruct germlines", "Format clones", "Building trees" ], "created": "2023-07-11 18:34:21", "modified": "2026-03-26 15:38:43", "commits": 29 }, { "source": "Discrete-Trait-Vignette.Rmd", "filename": "Discrete-Trait-Vignette.html", "title": "Discrete trait analysis", "author": "Kenneth B. Hoehn", "engine": "knitr::rmarkdown", "headings": [ "Discrete trait statistics", "Caveats and interpreting results", "Setting up IgPhyML", "Set up data structures and trees", "Visualize maximum parsimony trait reconstruction", "Discrete trait analysis with fixed trees", "Accounting for uncertainty in tree topology", "Within and between lineage permutations", "Controlling false positive rate through downsampling", "Incorporating switching constraints" ], "created": "2022-03-26 00:27:14", "modified": "2024-11-05 16:11:31", "commits": 20 }, { "source": "Measurable-Evolution.Rmd", "filename": "Measurable-Evolution.html", "title": "Detect ongoing B cell evolution", "author": "Kenneth B. Hoehn", "engine": "knitr::rmarkdown", "headings": [ "Date randomization test", "Set up data structures and trees", "Perform date randomization test", "Plot trees" ], "created": "2022-07-14 08:50:56", "modified": "2026-03-26 15:20:00", "commits": 10 }, { "source": "Plotting-Trees-Vignette.Rmd", "filename": "Plotting-Trees-Vignette.html", "title": "Plot B cell lineage trees", "author": "Kenneth B. Hoehn", "engine": "knitr::rmarkdown", "headings": [ "Basic plotting", "Plotting metadata", "Using ggtree and ggplot functions", "Editing all trees at once", "Saving trees to a file" ], "created": "2021-07-14 16:15:14", "modified": "2023-12-21 21:06:27", "commits": 9 }, { "source": "Quickstart-Vignette.Rmd", "filename": "Quickstart-Vignette.html", "title": "Dowser: Simple lineage tree construction", "author": "Kenneth B. Hoehn", "engine": "knitr::rmarkdown", "headings": [], "created": "2020-04-30 05:14:16", "modified": "2023-10-25 14:27:50", "commits": 11 }, { "source": "Germlines-Vignette.Rmd", "filename": "Germlines-Vignette.html", "title": "Reconstruct clonal germline sequences", "author": "Kenneth B. Hoehn", "engine": "knitr::rmarkdown", "headings": [ "Identify clonal clusters", "Obtain IMGT-gapped sequences", "Construct clonal germlines" ], "created": "2021-07-14 16:15:14", "modified": "2025-07-23 17:08:08", "commits": 12 }, { "source": "Sequences-Vignette.Rmd", "filename": "Sequences-Vignette.html", "title": "Reconstruct intermediate sequences", "author": "Kenneth B. Hoehn", "engine": "knitr::rmarkdown", "headings": [ "Saving sequences to a file" ], "created": "2021-07-14 16:15:14", "modified": "2024-10-18 21:36:35", "commits": 9 }, { "source": "NonB-Cell-Data.Rmd", "filename": "NonB-Cell-Data.html", "title": "Using data from non-B cells", "author": "Kenneth B. 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