Files in dowser

B Cell Receptor Phylogenetics Toolkit

NEWS.md README.md R/Statistics.R R/TreeFunctions.R R/Classes.R R/Clones.R R/Dowser.R R/Germlines.R R/Plotting.R R/Data.R R/TimeTreesFunctions.R R/zzz.R inst/doc/Germlines-Vignette.R inst/doc/Sequences-Vignette.R inst/doc/Plotting-Trees-Vignette.R inst/doc/NonB-Cell-Data.R inst/doc/Building-Time-Trees-Vignette.R inst/doc/Building-Time-Trees-Vignette.Rmd inst/doc/Building-Trees-Vignette.Rmd inst/doc/Measurable-Evolution.Rmd inst/doc/Quickstart-Vignette.pdf inst/doc/Resolve-Light-Chains-Vignette.R inst/doc/Discrete-Trait-Vignette.pdf inst/doc/Quickstart-Vignette.Rmd inst/doc/Germlines-Vignette.pdf inst/doc/Resolve-Light-Chains-Vignette.pdf inst/doc/Measurable-Evolution.pdf inst/doc/Germlines-Vignette.Rmd inst/doc/Building-Trees-Vignette.pdf inst/doc/Resolve-Light-Chains-Vignette.Rmd inst/doc/NonB-Cell-Data.Rmd inst/doc/Quickstart-Vignette.R inst/doc/Discrete-Trait-Vignette.R inst/doc/Building-Trees-Vignette.R inst/doc/Sequences-Vignette.pdf inst/doc/Measurable-Evolution.R inst/doc/Building-Time-Trees-Vignette.pdf inst/doc/Plotting-Trees-Vignette.Rmd inst/doc/Discrete-Trait-Vignette.Rmd inst/doc/Plotting-Trees-Vignette.pdf inst/doc/Sequences-Vignette.Rmd vignettes/Building-Time-Trees-Vignette.Rmd vignettes/Building-Trees-Vignette.Rmd vignettes/Measurable-Evolution.Rmd vignettes/Quickstart-Vignette.Rmd vignettes/Germlines-Vignette.Rmd vignettes/Resolve-Light-Chains-Vignette.Rmd vignettes/NonB-Cell-Data.Rmd vignettes/Plotting-Trees-Vignette.Rmd vignettes/Discrete-Trait-Vignette.Rmd vignettes/Sequences-Vignette.Rmd man/write_clone_to_xml.Rd man/getBootstraps.Rd man/buildGermline.Rd man/maskSequences.Rd man/IsotypeTrees.Rd man/BiopsyTrees.Rd man/readFasta.Rd man/writeLineageFile.Rd man/getSubTaxa.Rd man/create_traitset.Rd man/create_MRCA_prior_observed.Rd man/ExampleAirr.Rd man/checkDivergence.Rd man/airrClone-class.Rd man/dowser-package.Rd man/runCorrelationTest.Rd man/create_max_height_prior.Rd man/findSwitches.Rd man/create_starting_tree.Rd man/getAllSeqs.Rd man/getPalette.Rd man/stopCodonCheck.Rd man/sampleCloneMultiGroup.Rd man/getGermline.Rd man/buildPratchet.Rd man/createGermlines.Rd man/create_root_freqs.Rd man/ExampleMixedClones.Rd man/buildClonalGermline.Rd man/create_alignment.Rd man/buildPML.Rd man/buildRAxML.Rd man/readIMGT.Rd man/downsampleClone.Rd man/colorTrees.Rd man/readModelFile.Rd man/write_clones_to_xmls.Rd man/calcRF.Rd man/collapseNodes.Rd man/getNodeSeq.Rd man/reconIgPhyML.Rd man/resolveLightChains.Rd man/makeModelFile.Rd man/TimeTrees.Rd man/sampleClones.Rd man/getDivergence.Rd man/dowser.Rd man/getSeq.Rd man/condenseTrees.Rd man/buildPhylo.Rd man/correlationTest.Rd man/dfToFasta.Rd man/bootstrapTrees.Rd man/getSubclones.Rd man/ExampleMixedDb.Rd man/getTimeTreesIterate.Rd man/ExampleDbChangeo.Rd man/scaleBranches.Rd man/rerootTree.Rd man/testPS.Rd man/ExampleClones.Rd man/treesToPDF.Rd man/plotTrees.Rd man/buildBeast.Rd man/ExampleAirrTyCHE.Rd man/makeAirrClone.Rd man/create_MRCA_prior_germline.Rd man/testSC.Rd man/makeSkyline.Rd man/writeCloneSequences.Rd man/exportTrees.Rd man/stitchVDJ.Rd man/maskCodons.Rd man/readLineages.Rd man/plotSkylines.Rd man/testSP.Rd man/getTimeTrees.Rd man/getSkylines.Rd man/readBEAST.Rd man/stitchRegions.Rd man/buildIgphyml.Rd man/create_height_prior.Rd man/resolvePolytomies.Rd man/getTrees.Rd man/formatClones.Rd