├── .DS_Store ├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── ClusterDR.R ├── CreateSeuratObj.R ├── DotPlotTopGenes.R ├── HeatMapTopGenes.R ├── Plotting.R ├── RunDiffusion.R ├── RunDoubletfinder.R ├── RunQC.R ├── SlingShot.R ├── Utilities.R ├── getClusterMarkers.R ├── getMaxDim.R ├── ligrec.R ├── markerGenes_human.R ├── markerGenes_mouse.R ├── plotLRHeatmap.R ├── plotLRnetwork.R ├── processExper.R └── runtopgene.R ├── README.md ├── RunSeurat_fullscript.R ├── SeuratExtras.Rproj ├── data ├── Hs_PairsLigRec.RData ├── Mm_PairsLigRec.RData ├── colorpallette.RData ├── mouse_human.csv └── mouseortholog.RData └── man ├── BiGenePlot.Rd ├── ClusterDR.Rd ├── CurvePlot.Rd ├── DimPCAPlot.Rd ├── DotPlotTopGenes.Rd ├── HeatMapTopGenes.Rd ├── LineageFeaturePlot.Rd ├── PCAPwPlot.Rd ├── PCATools.Rd ├── RunDiffusion.Rd ├── RunDoubletfinder.Rd ├── RunLigRec.Rd ├── RunQC.Rd ├── SplitMetaPlot.Rd ├── celltypeVlnPlot.Rd ├── getClusterMarkers.Rd ├── getMaxDim.Rd ├── getSDS.Rd ├── lineageDimPlot.Rd ├── make3dPlot.Rd ├── plotLRHeatmap.Rd ├── plotLRnetwork.Rd ├── plotLineageHeatMap.Rd ├── plotLineangeGene.Rd ├── processExper.Rd ├── projectname-Project-name.Rd ├── runPseudoTimeDGE.Rd ├── runSlingshot.Rd ├── runtopgene.Rd ├── sampleBarGraph.Rd └── setSDS.Rd /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Morriseylab/scExtras/HEAD/.DS_Store -------------------------------------------------------------------------------- /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Morriseylab/scExtras/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Morriseylab/scExtras/HEAD/.gitignore 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