API for alakazam
Immunoglobulin Clonal Lineage and Diversity Analysis
| Global functions | |
|---|---|
| .onAttach | Source code |
| ABBREV_AA | Man page |
| AbundanceCurve | Man page |
| AbundanceCurve-class | Man page |
| AbundanceCurve-method | Man page |
| ChangeoClone | Man page |
| ChangeoClone-class | Man page |
| DEFAULT_COLORS | Man page |
| DNA_COLORS | Man page |
| DNA_IUPAC | Man page |
| DiversityCurve | Man page |
| DiversityCurve-class | Man page |
| DiversityCurve-method | Man page |
| EdgeTest | Man page |
| EdgeTest-class | Man page |
| EdgeTest-method | Man page |
| Example10x | Man page |
| ExampleDb | Man page |
| ExampleDbChangeo | Man page |
| ExampleTrees | Man page |
| IG_COLORS | Man page |
| IMGT_REGIONS | Man page |
| IUPAC_AA | Man page |
| IUPAC_CODES | Man page |
| IUPAC_DNA | Man page |
| MRCATest | Man page |
| MRCATest-class | Man page |
| MRCATest-method | Man page |
| SingleDb | Man page |
| TR_COLORS | Man page |
| _PACKAGE | Man page |
| adjustObservedAbundance | Source code |
| alakazam | Man page |
| alakazam-package | Man page |
| aliphatic | Man page Source code |
| alphaDiversity | Man page Source code |
| aminoAcidProperties | Man page Source code |
| baseTheme | Man page Source code |
| betaDiversity | Source code |
| bootstrapAbundance | Source code |
| buildPhylipLineage | Man page Source code |
| bulk | Man page Source code |
| calcChao1Coverage | Source code |
| calcCoverage | Man page Source code |
| calcDiversity | Man page Source code |
| calcSequenceAlignmentQuality | Source code |
| charge | Man page Source code |
| checkColumns | Man page Source code |
| checkPhylipOutput | Source code |
| collapseDuplicates | Man page Source code |
| combineIgphyml | Man page Source code |
| countClones | Man page Source code |
| countDeleted | Source code |
| countGenes | Man page Source code |
| countOccurrences | Source code |
| countPatterns | Man page Source code |
| cpuCount | Man page Source code |
| estimateAbundance | Man page Source code |
| extractVRegion | Man page Source code |
| getAAMatrix | Man page Source code |
| getAllVJL | Source code |
| getAllele | Man page Source code |
| getChain | Man page Source code |
| getDNAMatrix | Man page Source code |
| getFamily | Man page Source code |
| getGene | Man page Source code |
| getLocus | Man page Source code |
| getMRCA | Man page Source code |
| getPathLengths | Man page Source code |
| getPhylipEdges | Source code |
| getPhylipInferred | Source code |
| getPositionQuality | Man page Source code |
| getSegment | Man page Source code |
| graphToPhylo | Man page Source code |
| gravy | Man page Source code |
| gridPlot | Man page Source code |
| groupGenes | Man page Source code |
| helperAlpha | Source code |
| helperBeta | Source code |
| helperTest | Source code |
| inferCompleteAbundance | Source code |
| inferRarefiedCoverage | Source code |
| inferRarefiedDiversity | Source code |
| inferUnseenAbundance | Source code |
| inferUnseenCount | Source code |
| isValidAASeq | Man page Source code |
| junctionAlignment | Man page Source code |
| lchooseStirling | Source code |
| makeChangeoClone | Man page Source code |
| makeTempDir | Man page Source code |
| maskPositionsByQuality | Man page Source code |
| maskSeqEnds | Man page Source code |
| maskSeqGaps | Man page Source code |
| modifyPhylipEdges | Source code |
| nonsquareDist | Man page Source code |
| nonsquareDistRcpp | Source code |
| padSeqEnds | Man page Source code |
| pairwiseDist | Man page Source code |
| pairwiseDistRcpp | Source code |
| pairwiseEqual | Man page Source code |
| permuteLabels | Man page Source code |
| phylipToGraph | Source code |
| phyloToGraph | Man page Source code |
| plot,AbundanceCurve,missing-method | Man page |
| plot,DiversityCurve,missing-method | Man page |
| plot,DiversityCurve,numeric-method | Man page |
| plot,EdgeTest,missing-method | Man page |
| plot,MRCATest,missing-method | Man page |
| plotAbundanceCurve | Man page Source code |
| plotDiversityCurve | Man page Source code |
| plotDiversityTest | Man page Source code |
| plotEdgeTest | Man page Source code |
| plotMRCATest | Man page Source code |
| plotSubtrees | Man page Source code |
| polar | Man page Source code |
| print,AbundanceCurve-method | Man page |
| print,DiversityCurve-method | Man page |
| print,EdgeTest-method | Man page |
| print,MRCATest-method | Man page |
| progressBar | Man page Source code |
| rarefyDiversity | Man page Source code |
| readChangeoDb | Man page Source code |
| readFastqDb | Man page Source code |
| readIgphyml | Man page Source code |
| readPhylipOutput | Source code |
| rerootGermline | Source code |
| runPhylip | Source code |
| seqDist | Man page Source code |
| seqDistRcpp | Source code |
| seqEqual | Man page Source code |
| sequenceAlignmentQuality | Source code |
| sortGenes | Man page Source code |
| stoufferMeta | Man page Source code |
| summarizeSubtrees | Man page Source code |
| tableEdges | Man page Source code |
| testDiversity | Man page Source code |
| testEdges | Man page Source code |
| testMRCA | Man page Source code |
| translateDNA | Man page |
| translateStrings | Man page Source code |
| writeChangeoDb | Man page Source code |
| writePhylipInput | Source code |
