Files in alakazam

Immunoglobulin Clonal Lineage and Diversity Analysis

NEWS.md README.md R/RcppExports.R R/Diversity.R R/Gene.R R/Alakazam.R R/Topology.R R/Classes.R R/Fastq.R R/Core.R R/Sequence.R R/Data.R R/Deprecated.R R/AminoAcids.R R/Lineage.R inst/doc/Fastq-Vignette.pdf inst/doc/Topology-Vignette.R inst/doc/Files-Vignette.R inst/doc/Files-Vignette.pdf inst/doc/AminoAcids-Vignette.pdf inst/doc/Diversity-Vignette.Rmd inst/doc/Topology-Vignette.Rmd inst/doc/GeneUsage-Vignette.R inst/doc/Lineage-Vignette.R inst/doc/GeneUsage-Vignette.Rmd inst/doc/GeneUsage-Vignette.pdf inst/doc/Diversity-Vignette.R inst/doc/AminoAcids-Vignette.Rmd inst/doc/Fastq-Vignette.Rmd inst/doc/Lineage-Vignette.Rmd inst/doc/Topology-Vignette.pdf inst/doc/AminoAcids-Vignette.R inst/doc/Lineage-Vignette.pdf inst/doc/Diversity-Vignette.pdf inst/doc/Files-Vignette.Rmd inst/doc/Fastq-Vignette.R vignettes/Diversity-Vignette.Rmd vignettes/Topology-Vignette.Rmd vignettes/GeneUsage-Vignette.Rmd vignettes/AminoAcids-Vignette.Rmd vignettes/Fastq-Vignette.Rmd vignettes/Lineage-Vignette.Rmd vignettes/Files-Vignette.Rmd man/Example10x.Rd man/maskSeqGaps.Rd man/rarefyDiversity.Rd man/stoufferMeta.Rd man/isValidAASeq.Rd man/EdgeTest-class.Rd man/ChangeoClone-class.Rd man/maskSeqEnds.Rd man/polar.Rd man/plotAbundanceCurve.Rd man/seqDist.Rd man/sortGenes.Rd man/getSegment.Rd man/ExampleDb.Rd man/plotMRCATest.Rd man/IUPAC_CODES.Rd man/IMGT_REGIONS.Rd man/MRCATest-class.Rd man/readIgphyml.Rd man/translateStrings.Rd man/maskPositionsByQuality.Rd man/translateDNA.Rd man/gravy.Rd man/testMRCA.Rd man/countGenes.Rd man/DEFAULT_COLORS.Rd man/pairwiseDist.Rd man/graphToPhylo.Rd man/testEdges.Rd man/estimateAbundance.Rd man/plotSubtrees.Rd man/aminoAcidProperties.Rd man/buildPhylipLineage.Rd man/permuteLabels.Rd man/getDNAMatrix.Rd man/cpuCount.Rd man/countClones.Rd man/seqEqual.Rd man/plotDiversityTest.Rd man/tableEdges.Rd man/getMRCA.Rd man/baseTheme.Rd man/ExampleTrees.Rd man/SingleDb.Rd man/charge.Rd man/bulk.Rd man/writeChangeoDb.Rd man/getAAMatrix.Rd man/summarizeSubtrees.Rd man/getPathLengths.Rd man/junctionAlignment.Rd man/checkColumns.Rd man/calcDiversity.Rd man/countPatterns.Rd man/calcCoverage.Rd man/ExampleDbChangeo.Rd man/alakazam.Rd man/pairwiseEqual.Rd man/ABBREV_AA.Rd man/alphaDiversity.Rd man/makeTempDir.Rd man/padSeqEnds.Rd man/combineIgphyml.Rd man/groupGenes.Rd man/AbundanceCurve-class.Rd man/alakazam-package.Rd man/progressBar.Rd man/readFastqDb.Rd man/getPositionQuality.Rd man/extractVRegion.Rd man/phyloToGraph.Rd man/readChangeoDb.Rd man/plotDiversityCurve.Rd man/gridPlot.Rd man/makeChangeoClone.Rd man/collapseDuplicates.Rd man/nonsquareDist.Rd man/DiversityCurve-class.Rd man/testDiversity.Rd man/plotEdgeTest.Rd man/aliphatic.Rd