API for olli0601/phyloscan

Global functions
onAttach Source code
onLoad Source code
phsc.bam.get.length.and.pos.of.mergedreads Source code
phsc.cmd.LikelyTransmissions Source code
phsc.cmd.LikelyTransmissionsSummary Source code
phsc.cmd.NormalisationLookupWriter Source code
phsc.cmd.SplitPatientsToSubGraphs Source code
phsc.cmd.SplitPatientsToSubtrees Source code
phsc.cmd.SummaryStatistics Source code
phsc.cmd.bam.calculate.read.distribution Source code
phsc.cmd.blacklist.downsample Source code
phsc.cmd.blacklist.dualinfections Source code
phsc.cmd.blacklist.parsimonybased Source code
phsc.cmd.blacklist.reads Source code
phsc.cmd.blacklist.rogue.extremeprob Source code
phsc.cmd.blacklist.rogue.geneticdistance Source code
phsc.cmd.mafft.add Source code
phsc.cmd.pairwise.relationships Source code
phsc.cmd.phyloscanner.multi Source code
phsc.cmd.phyloscanner.one Source code
phsc.cmd.phyloscanner.one.resume Source code
phsc.cmd.process.phyloscanner.output.in.directory Source code
phsc.cmd.read.processed.phyloscanner.output.in.directory Source code
phsc.combine.phyloscanner.output Source code
phsc.drop.tip Source code
phsc.extract.clade Source code
phsc.get.assignments.by.window.for.couple Source code
phsc.get.basic.pairwise.relationships Source code
phsc.get.maximum.probability.transmission.network Source code
phsc.get.maximum.probability.transmission.network.RBGLedmonds Source code
phsc.get.maximum.probability.transmission.network.greedy Source code
phsc.get.pairwise.relationships Source code
phsc.get.pairwise.relationships.keff.and.neff Source code
phsc.get.pairwise.relationships.likelihoods Source code
phsc.get.pairwise.relationships.numbers Source code
phsc.get.pairwise.relationships.posterior Source code
phsc.get.prior.parameter.n0 Source code
phsc.phy.collapse.monophyletic.clades Source code
phsc.plot.default.colours.for.relationtypes Source code
phsc.plot.max.probability.network Source code
phsc.plot.phy.selected.individuals Source code
phsc.plot.phy.selected.pairs Source code
phsc.plot.phycollapsed.selected.individuals Source code
phsc.plot.probability.network Source code
phsc.plot.windowassignments.by.runs Source code
phsc.plot.windowscan.for.pairs Source code
phsc.plot.windowsummaries.for.pairs Source code
phsc.read.likelytransmissions Source code
phsc.read.processed.phyloscanner.output.in.directory Source code
phsc.read.subtrees Source code
phsc.read.trees Source code
simplify.summary Source code
olli0601/phyloscan documentation built on Sept. 4, 2018, 12:05 p.m.