API for dowser
B Cell Receptor Phylogenetics Toolkit
| Global functions | |
|---|---|
| .onAttach | Source code |
| BiopsyTrees | Man page |
| ExampleAirr | Man page |
| ExampleAirrTyCHE | Man page |
| ExampleClones | Man page |
| ExampleDbChangeo | Man page |
| ExampleMixedClones | Man page |
| ExampleMixedDb | Man page |
| IsotypeTrees | Man page |
| TimeTrees | Man page |
| airrClone | Man page |
| airrClone-class | Man page |
| bootstrapClones | Source code |
| bootstrapTrees | Man page Source code |
| buildAllClonalGermlines | Man page Source code |
| buildBeast | Man page Source code |
| buildClonalGermline | Man page Source code |
| buildGermline | Man page Source code |
| buildIgphyml | Man page Source code |
| buildPML | Man page Source code |
| buildPhylo | Man page Source code |
| buildPratchet | Man page Source code |
| buildRAxML | Man page Source code |
| calcRF | Man page Source code |
| callOlga | Source code |
| checkDivergence | Man page Source code |
| checkGenesUCA | Source code |
| checkNodeDivergences | Man page Source code |
| cleanAlignment | Source code |
| cleanUpIterateResume | Source code |
| cloneToFasta | Source code |
| collapseNodes | Man page Source code |
| colorTrees | Man page Source code |
| combineColors | Source code |
| compute_germlines | Source code |
| condenseTrees | Man page Source code |
| consensus_tree | Source code |
| correlationTest | Man page Source code |
| createAllGermlines | Man page Source code |
| createGermlines | Man page Source code |
| create_MRCA_prior_germline | Man page Source code |
| create_MRCA_prior_observed | Man page Source code |
| create_alignment | Man page Source code |
| create_height_prior | Man page Source code |
| create_max_height_prior | Man page Source code |
| create_root_freqs | Man page Source code |
| create_starting_tree | Man page Source code |
| create_traitset | Man page Source code |
| dataColumnEqual | Source code |
| dataFrameToRecords | Source code |
| dataFrameToValueRows | Source code |
| dfToFasta | Man page Source code |
| downsampleClone | Man page Source code |
| dowser | Man page |
| dowser-package | Man page |
| dowserObjectEquivalent | Man page Source code |
| exportTrees | Man page Source code |
| filterCombs | Man page Source code |
| filterPartialSeqs | Man page Source code |
| findConsensus | Source code |
| findSwitches | Man page Source code |
| formatClones | Man page Source code |
| getAllSeqs | Man page Source code |
| getBootstraps | Man page Source code |
| getClonesToResume | Source code |
| getDiffPoint | Man page Source code |
| getDiffPoints | Man page Source code |
| getDivergence | Man page Source code |
| getGermline | Man page Source code |
| getHeightsAndLengths | Man page Source code |
| getNodeSeq | Man page Source code |
| getPalette | Man page Source code |
| getSeq | Man page Source code |
| getSeqPath | Man page Source code |
| getSkylines | Man page Source code |
| getSubTaxa | Man page Source code |
| getSubclones | Man page Source code |
| getTimeTrees | Man page Source code |
| getTimeTreesIterate | Man page Source code |
| getTreeTable | Source code |
| getTrees | Man page Source code |
| getTreesAndUCAs | Man page Source code |
| get_starting_junction | Source code |
| installPythonDependencies | Man page Source code |
| listToPmlParams | Source code |
| makeAirrClone | Man page Source code |
| makeModelFile | Man page Source code |
| makeSkyline | Man page Source code |
| makeTrees | Source code |
| make_locus_checker | Source code |
| mapSubtrees | Man page Source code |
| maskAmbiguousReferenceSites | Source code |
| maskCodons | Man page Source code |
| maskSequences | Man page Source code |
| matching_function_parallel | Source code |
| nexusTreeWithTranslate | Source code |
| plotMSA | Man page Source code |
| plotSkylines | Man page Source code |
| plotTrees | Man page Source code |
| pmlParamsEqual | Source code |
| pmlParamsToList | Source code |
| processCloneGermline | Source code |
| processClones | Source code |
| readBEAST | Man page Source code |
| readFasta | Man page Source code |
| readIMGT | Man page Source code |
| readLineages | Man page Source code |
| readModelFile | Man page Source code |
| readSwitches | Source code |
| readTreesJSON | Man page Source code |
| readUcaLhood | Source code |
| reconIgPhyML | Man page Source code |
| rerootTree | Man page Source code |
| resolveLightChains | Man page Source code |
| resolvePolytomies | Man page Source code |
| runCorrelationTest | Man page Source code |
| sampleCloneMultiGroup | Man page Source code |
| sampleClones | Man page Source code |
| saveIteration | Source code |
| scaleBranches | Man page Source code |
| setNodeDivergences | Man page Source code |
| setUpIterateResume | Source code |
| splits_func | Source code |
| stitchRegions | Man page Source code |
| stitchVDJ | Man page Source code |
| stopCodonCheck | Man page Source code |
| testPS | Man page Source code |
| testSC | Man page Source code |
| testSP | Man page Source code |
| treesEquivalent | Man page Source code |
| treesToPDF | Man page Source code |
| updateClone | Source code |
| writeCloneSequences | Man page Source code |
| writeFasta | Man page Source code |
| writeLineageFile | Man page Source code |
| writePosteriorTreeList | Source code |
| writeTreesJSON | Man page Source code |
| write_clone_to_xml | Man page Source code |
| write_clones_to_xmls | Man page Source code |
