Files in dowser
B Cell Receptor Phylogenetics Toolkit
MD5
NEWS.md
README.md
NAMESPACE
DESCRIPTION
R/Statistics.R
R/TreeFunctions.R
R/Classes.R
R/Clones.R
R/Dowser.R
R/Germlines.R
R/Plotting.R
R/IO.R
R/Data.R
R/TimeTreesFunctions.R
R/zzz.R
inst/CITATION
inst/get_UCA.py
inst/doc/Plotting-Trees-Vignette.R
inst/doc/Building-Time-Trees-Vignette.R
inst/doc/Building-Time-Trees-Vignette.Rmd
inst/doc/Building-Trees-Vignette.Rmd
inst/doc/Quickstart-Vignette.pdf
inst/doc/Input-Output-Vignette.pdf
inst/doc/Quickstart-Vignette.Rmd
inst/doc/Input-Output-Vignette.R
inst/doc/Building-Trees-Vignette.pdf
inst/doc/Quickstart-Vignette.R
inst/doc/Building-Trees-Vignette.R
inst/doc/Building-Time-Trees-Vignette.pdf
inst/doc/Plotting-Trees-Vignette.Rmd
inst/doc/Plotting-Trees-Vignette.pdf
inst/doc/Input-Output-Vignette.Rmd
inst/extdata/germlines/imgt/IMGT.yaml
inst/extdata/germlines/imgt/human/vdj/imgt_human_IGHV.fasta
inst/extdata/germlines/imgt/human/vdj/imgt_human_IGHD.fasta
inst/extdata/germlines/imgt/human/vdj/imgt_human_IGHJ.fasta
build/vignette.rds
build/partial.rdb
vignettes/Building-Time-Trees-Vignette.Rmd
vignettes/Building-Trees-Vignette.Rmd
vignettes/Quickstart-Vignette.Rmd
vignettes/Plotting-Trees-Vignette.Rmd
vignettes/Input-Output-Vignette.Rmd
data/BiopsyTrees.rda
data/ExampleAirr.rda
data/ExampleAirrTyCHE.rda
data/ExampleMixedDb.rda
data/ExampleMixedClones.rda
data/TimeTrees.rda
data/IsotypeTrees.rda
data/ExampleClones.rda
data/ExampleDbChangeo.rda
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/plotMSA.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/writeFasta.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/treesEquivalent.Rd
man/getDivergence.Rd
man/getDiffPoints.Rd
man/getHeightsAndLengths.Rd
man/dowser.Rd
man/writeTreesJSON.Rd
man/getSeq.Rd
man/condenseTrees.Rd
man/filterCombs.Rd
man/createAllGermlines.Rd
man/buildPhylo.Rd
man/getSeqPath.Rd
man/mapSubtrees.Rd
man/correlationTest.Rd
man/dfToFasta.Rd
man/readTreesJSON.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/filterPartialSeqs.Rd
man/ExampleClones.Rd
man/getTreesAndUCAs.Rd
man/treesToPDF.Rd
man/plotTrees.Rd
man/buildBeast.Rd
man/buildAllClonalGermlines.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/installPythonDependencies.Rd
man/readLineages.Rd
man/setNodeDivergences.Rd
man/plotSkylines.Rd
man/testSP.Rd
man/getTimeTrees.Rd
man/getSkylines.Rd
man/readBEAST.Rd
man/stitchRegions.Rd
man/buildIgphyml.Rd
man/dowserObjectEquivalent.Rd
man/create_height_prior.Rd
man/getDiffPoint.Rd
man/checkNodeDivergences.Rd
man/resolvePolytomies.Rd
man/getTrees.Rd
man/formatClones.Rd
