API for wuaipinglab/sitePath
Phylogeny-based sequence clustering with site polymorphism
| Global functions | |
|---|---|
| .actualExtractSite | Source code |
| .annotateSNPonTree | Source code |
| .assignClusterNames | Source code |
| .calibrateFixedAA | Source code |
| .calibrateNode | Source code |
| .checkMinEffectiveSize | Source code |
| .checkSite | Source code |
| .childrenTips | Source code |
| .clusterByFixation | Source code |
| .collectParallelSites | Source code |
| .createCluster | Source code |
| .createSNPplot | Source code |
| .findAncestralNode | Source code |
| .findFixationPath | Source code |
| .findGroupingLinkage | Source code |
| .groupMutationsBySites | Source code |
| .mergeClusters | Source code |
| .mutationTable | Source code |
| .pathsUnderThreshold | Source code |
| .phyMSAmatch | Source code |
| .qualifiedFixation | Source code |
| .qualifiedMutAA | Source code |
| .runEntropyMinimization | Source code |
| .selectMutByAA | Source code |
| .siteColorScheme | Source code |
| .stablePathIndex | Source code |
| .tipSeqsAlongPathNodes | Source code |
| .unambiguousChars | Source code |
| .unifyEntropyGrouping | Source code |
| .unpackClustersByPath | Source code |
| SNPsites | Man page Source code |
| SNPsites.phyMSAmatched | Man page Source code |
| addMSA | Man page Source code |
| addMSA.phylo | Man page Source code |
| addMSA.treedata | Man page Source code |
| allSitesName | Man page Source code |
| allSitesName.SNPsites | Man page Source code |
| allSitesName.fixationSites | Man page Source code |
| allSitesName.paraFixSites | Man page Source code |
| allSitesName.parallelSites | Man page Source code |
| allSitesName.sitesMinEntropy | Man page Source code |
| as.data.frame.SNPsites | Man page Source code |
| as.data.frame.fixationSites | Man page Source code |
| as.data.frame.parallelSites | Man page Source code |
| as.phylo | Man page |
| as.phylo.fixationIndels | Source code |
| as.phylo.fixationSites | Source code |
| as.phylo.phyMSAmatched | Source code |
| as.phylo.sitePath | Source code |
| as.phylo.sitesMinEntropy | Source code |
| as.treedata | Man page |
| as.treedata.fixationIndels | Source code |
| as.treedata.fixationPath | Source code |
| as.treedata.fixationSites | Source code |
| divergentNode | Source code |
| extractSite | Man page Source code |
| extractSite.fixationSites | Man page Source code |
| extractSite.parallelSites | Source code |
| extractTips | Man page Source code |
| extractTips.fixationSites | Man page Source code |
| extractTips.lineagePath | Man page Source code |
| extractTips.parallelSites | Man page Source code |
| extractTips.sitePara | Man page Source code |
| extractTips.sitePath | Man page Source code |
| extractTips.sitesMinEntropy | Man page Source code |
| fixationIndels | Man page Source code |
| fixationIndels.sitesMinEntropy | Man page Source code |
| fixationPath | Man page Source code |
| fixationPath.fixationSites | Man page Source code |
| fixationPath.sitesMinEntropy | Man page Source code |
| fixationSites | Man page Source code |
| fixationSites.lineagePath | Man page Source code |
| fixationSites.paraFixSites | Man page Source code |
| fixationSites.sitesMinEntropy | Man page Source code |
| getReference | Source code |
| getSimilarityMatrix | Source code |
| groupTips | Man page Source code |
| groupTips.fixationPath | Man page Source code |
| groupTips.fixationSites | Man page Source code |
| groupTips.lineagePath | Man page Source code |
| groupTips.phyMSAmatched | Man page Source code |
| groupTips.sitesMinEntropy | Man page Source code |
| h3n2_align | Man page |
| h3n2_align_reduced | Man page |
| h3n2_tree | Man page |
| h3n2_tree_reduced | Man page |
| lineagePath | Man page Source code |
| lineagePath.paraFixSites | Man page Source code |
| lineagePath.phyMSAmatched | Man page Source code |
| lineagePath.phylo | Man page Source code |
| lineagePath.sneakPeekedPaths | Man page Source code |
| lineagePath.treedata | Man page Source code |
| majorSNPtips | Source code |
| mergePaths | Source code |
| minEntropyByComparing | Source code |
| minEntropyByDeleting | Source code |
| minEntropyByInserting | Source code |
| multiFixationSites | Man page Source code |
| multiFixationSites.lineagePath | Source code |
| pairSimilarity | Source code |
| paraFixSites | Man page Source code |
| paraFixSites.lineagePath | Man page Source code |
| paraFixSites.phylo | Man page Source code |
| paraFixSites.sitesMinEntropy | Man page Source code |
| paraFixSites.treedata | Man page Source code |
| parallelSites | Man page Source code |
| parallelSites.lineagePath | Man page Source code |
| parallelSites.paraFixSites | Man page Source code |
| parallelSites.sitesMinEntropy | Man page Source code |
| phyMSAmatched | Man page |
| plot.fixationIndels | Man page Source code |
| plot.fixationPath | Man page Source code |
| plot.fixationSites | Man page Source code |
| plot.lineagePath | Man page Source code |
| plot.parallelSites | Man page Source code |
| plot.phyMSAmatched | Man page Source code |
| plot.sitePath | Man page Source code |
| plotFixationSites | Man page Source code |
| plotFixationSites.fixationSites | Man page Source code |
| plotFixationSites.paraFixSites | Man page Source code |
| plotMutSites | Man page Source code |
| plotMutSites.SNPsites | Man page Source code |
| plotMutSites.fixationSites | Man page Source code |
| plotMutSites.lineagePath | Man page Source code |
| plotMutSites.paraFixSites | Man page Source code |
| plotMutSites.parallelSites | Man page Source code |
| plotParallelSites | Man page Source code |
| plotParallelSites.paraFixSites | Man page Source code |
| plotParallelSites.parallelSites | Man page Source code |
| plotSingleSite | Man page Source code |
| plotSingleSite.fixationSites | Man page Source code |
| plotSingleSite.lineagePath | Man page Source code |
| plotSingleSite.parallelSites | Man page Source code |
| plotSingleSite.sitesMinEntropy | Man page Source code |
| print.SNPsites | Source code |
| print.alignment | Source code |
| print.fixationIndels | Source code |
| print.fixationPath | Source code |
| print.fixationSites | Source code |
| print.indelPath | Source code |
| print.lineagePath | Source code |
| print.paraFixSites | Source code |
| print.parallelSites | Source code |
| print.phyMSAmatched | Source code |
| print.sitePara | Source code |
| print.sitePath | Source code |
| print.sitesMinEntropy | Source code |
| read.alignment | Man page |
| read.tree | Man page |
| reexports | Man page |
| sars2_align | Man page |
| sars2_tree | Man page |
| setSiteNumbering | Man page Source code |
| setSiteNumbering.fixationPath | Source code |
| setSiteNumbering.fixationSites | Source code |
| setSiteNumbering.paraFixSites | Source code |
| setSiteNumbering.phyMSAmatched | Man page Source code |
| similarityMatrix | Man page Source code |
| sitePath-deprecated | Man page |
| sitesMinEntropy | Man page Source code |
| sitesMinEntropy.lineagePath | Man page Source code |
| sneakPeek | Man page Source code |
| tableAA | Source code |
| terminalTipsByDist | Source code |
| terminalTipsBySim | Source code |
| zikv_align | Man page |
| zikv_align_reduced | Man page |
| zikv_tree | Man page |
| zikv_tree_reduced | Man page |
