├── .gitattributes ├── DESCRIPTION ├── LICENSE.pdf ├── NAMESPACE ├── R ├── backtrack.R ├── calcDistMatrix.R ├── globalAlign2.R ├── globalCostMatrix.R ├── interWeights.R ├── localAlign2.R ├── localAlignAutoThreshold.R ├── mappingActualData.R ├── myLocalMinima.R ├── myStepPattern.R ├── mySub2Ind.R ├── myWindow.R ├── plotAlignment.R ├── pseudotimeClust.R └── scaleInterpolate.R ├── README.md ├── Rplots.pdf ├── data ├── datalist ├── expGlobalLPS.txt ├── expGlobalPAM.txt ├── expLocalLPS.txt ├── expLocalPAM.txt ├── trajLPS.txt └── trajPAM.txt ├── man ├── calcDistMat.Rd ├── findGlobalMinima.Rd ├── findLocalMinima.Rd ├── globalAlign.Rd ├── ind2sub.Rd ├── interWeights.Rd ├── localAlign.Rd ├── localAlignAutoThreshold.Rd ├── mapRealDataGlobal.Rd ├── mapRealDataLocal.Rd ├── plotAlign.Rd ├── plotMapping.Rd ├── pseudotimeClust.Rd ├── scaleInterpolate.Rd └── sub2ind.Rd └── src ├── Makevars ├── Makevars.win └── computeCM.c /.gitattributes: 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