Package: dowser 2.2.1.999

dowser: B Cell Receptor Phylogenetics Toolkit

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees. Provides methods to 1) reconstruct unmutated ancestral sequences, 2) build B cell phylogenetic trees using multiple methods, 3) visualize trees with metadata at the tips, 4) reconstruct intermediate sequences, 5) detect biased ancestor-descendant relationships among metadata types Workflow examples available at documentation site (see URL). Citations: Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>, Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.

Authors:Kenneth Hoehn [aut, cre], Cole Jensen [ctb], Susanna Marquez [ctb], Jason Vander Heiden [ctb], Steven Kleinstein [aut, cph]

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dowser.pdf |dowser.html✨
dowser/json (API)
NEWS

# Install 'dowser' in R:
install.packages('dowser', repos = c('https://kbhoehn.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://bitbucket.org/kleinstein/dowser

Datasets:

On CRAN:

50 exports 1.97 score 121 dependencies 54 scripts 378 downloads

Last updated 13 hours agofrom:1008c47058. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 17 2024
R-4.5-winWARNINGSep 17 2024
R-4.5-linuxWARNINGSep 17 2024
R-4.4-winWARNINGSep 17 2024
R-4.4-macWARNINGSep 17 2024
R-4.3-winWARNINGSep 17 2024
R-4.3-macWARNINGSep 17 2024

Exports:addGapsassignGenesbootstrapTreesbuildIgphymlbuildPhylobuildPMLbuildPratchetbuildRAxMLcalcRFcollapseNodescolorTreescondenseTreescorrelationTestcreateGermlinesdfToFastadownloadIMGTdownsampleCloneexportTreesfindSwitchesformatClonesgetBootstrapsgetDivergencegetNodeSeqgetPalettegetSeqgetSubclonesgetSubTaxagetTreesimgtToIgblastmakeAirrClonemakeModelFilemaskCodonsmaskSequencesplotTreesreadFastareadIMGTreadLineagesreadModelFilereconIgPhyMLrerootTreeresolveLightChainsresolvePolytomiesscaleBranchestestPStestSCtestSPtreesToPDFwriteCloneSequenceswriteFastawriteLineageFile

Dependencies:abindade4airralakazamapeaplotaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsclicliprcodetoolscolorspacecommonmarkcpp11crayoncurlDelayedArraydigestdiptestdoParalleldplyrfansifarverfastmatchforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggfunggplot2ggplotifyggtreegluegridExtragridGraphicsgtablehmshttrigraphIRangesisobanditeratorsjsonliteKernSmoothlabelinglambda.rlatticelazyevallifecyclemagrittrmarkdownMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpatchworkphangornphylotatepillarpixmappkgconfigprettyunitsprogresspurrrquadprogR6RColorBrewerRcppRcppArmadilloreadrRhtslibrlangRsamtoolsS4ArraysS4VectorsscalessegmentedseqinrshazamsnowspSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttidytreetreeiotzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXVectoryamlyulab.utilszlibbioc

Build B cell lineage trees

Kenneth B. Hoehn

Rendered fromBuilding-Trees-Vignette.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2023-12-06
Started: 2021-07-14

Building trees with paired heavy and light chain data

Cole G. Jensen

Rendered fromResolve-Light-Chains-Vignette.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2023-12-21
Started: 2023-07-11

Discrete trait analysis

Kenneth B. Hoehn

Rendered fromDiscrete-Trait-Vignette.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2023-12-21
Started: 2022-03-26

Detect ongoing B cell evolution

Kenneth B. Hoehn

Rendered fromMeasurable-Evolution.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2023-03-13
Started: 2022-07-14

Plot B cell lineage trees

Kenneth B. Hoehn

Rendered fromPlotting-Trees-Vignette.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2023-12-21
Started: 2021-07-14

Dowser: Simple lineage tree construction

Kenneth B. Hoehn

Rendered fromQuickstart-Vignette.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2023-10-25
Started: 2020-04-30

Reconstruct clonal germline sequences

Kenneth B. Hoehn

Rendered fromGermlines-Vignette.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2023-09-06
Started: 2021-07-14

Reconstruct intermediate sequences

Kenneth B. Hoehn

Rendered fromSequences-Vignette.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2023-03-13
Started: 2021-07-14

Readme and manuals

Help Manual

Help pageTopics
'addGaps' Add IMGT gaps to IgBlast outputaddGaps
S4 class defining a clone in DowserairrClone airrClone-class
'assignGenes' Runs IgBlast on a fasta fileassignGenes
Example Ig lineage trees with biopsy reconstructions.BiopsyTrees
Deprecated! Please use findSwitches instead.bootstrapTrees
'buildClonalGermline' Determine consensus clone sequence and create germline for clonebuildClonalGermline
'buildGermline' reconstruct germline segments from alignment databuildGermline
Wrapper to build IgPhyML trees and infer intermediate nodesbuildIgphyml
Wrapper for alakazam::buildPhylipLineagebuildPhylo
Wrapper for phangorn::optim.pmlbuildPML
Wrapper for phangorn::pratchetbuildPratchet
Wrapper to build RAxML-ng trees and infer intermediate nodesbuildRAxML
Finds the Robinson-Fould's cluster distance between phylogenies.calcRF
Collapse internal nodes with the same predicted sequencecollapseNodes
Get a color palette for a predefined set of trait valuescolorTrees
Condense a set of equally parsimonious node labels into a single treecondenseTrees
Run date randomization test for temporal signal on a set of trees.correlationTest
createGermlines Determine consensus clone sequence and create germline for clonecreateGermlines
Write a fasta file of sequences 'readFasta' reads a fasta filedfToFasta
'downloadIMGT' Download IMGT GENE-DB databasesdownloadIMGT
'downsampleClone' Down-sample clone to maximum tip/switch ratiodownsampleClone
The dowser packagedowser
Example AIRR databaseExampleAirr
Example Ig lineage treesExampleClones
Example Change-O databaseExampleDbChangeo
Example Multiple Partition TreesExampleMixedClones
Example Change-O databaseExampleMixedDb
Exports the phylogentic trees from the airrClone objectexportTrees
Create a bootstrap distribution for clone sequence alignments, and estimate trees for each bootstrap replicate.findSwitches
Generate an ordered list of airrClone objects for lineage constructionformatClones
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.getBootstraps
Get divergence from root of tree for each tipgetDivergence
getGermline get germline segment from specified receptor and segmentgetGermline
Return IMGT gapped sequence of specified tree nodegetNodeSeq
Get a color palette for a predefined set of trait values. 'Germline' defaults to black unless specified.getPalette
Deprecated! Use getNodeSeqgetSeq
#' Deprecated! Use resolveLightChainsgetSubclones
Get the tip labels as part of a clade defined by an internal nodegetSubTaxa
Estimate lineage tree topologies, branch lengths, and internal node states if desiredgetTrees
'imgtToIgblast' Format IMGT database to Igblast databaseimgtToIgblast
Example Ig lineage trees with isotype reconstructions.IsotypeTrees
Generate a airrClone object for lineage constructionmakeAirrClone
Make a parsimony model filemakeModelFile
'maskCodons' Masks codons split by insertionsmaskCodons
'maskSequences' Mask codons split by insertions in V genemaskSequences
Plot a tree with colored internal node labels using ggtreeplotTrees
Read a fasta file into a list of sequences 'readFasta' reads a fasta filereadFasta
'readIMGT' read in IMGT databasereadIMGT
Read in all trees from a lineages filereadLineages
Read in a parsimony model filereadModelFile
Do IgPhyML maximum parsimony reconstructionreconIgPhyML
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.rerootTree
Define subgroups within clones based on light chain rearrangementsresolveLightChains
Resolve polytomies to have the minimum number of single timepoint cladesresolvePolytomies
Run correlationTest, based on https://doi.org/10.1111/2041-210X.12466runCorrelationTest
Scale branch lengths to represent either mutations or mutations per site.scaleBranches
stitchRegions Similar to stitchVDJ but with segment IDs instead of nulecotidesstitchRegions
stitchVDJ combines germline gene segments to a single stringstitchVDJ
Performs PS (parsimony score) test on switch datatestPS
Performs SC (switch count) test on switch datatestSC
Performs SP (switch proportion) test on switch datatestSP
Example Ig lineage trees sampled over time.TimeTrees
Simple function for plotting a lot of trees into a pdftreesToPDF
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".writeCloneSequences
'writeFasta' Write a fasta file of sequences given a named list of sequenceswriteFasta
Write lineage file for IgPhyML usewriteLineageFile