├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── dataAccess.R ├── deTest.R ├── helperFx.R ├── runViz.R ├── sCVdataClass.R ├── scClustViz.R ├── shinyModules.R └── spreadLabels2.R ├── README.md ├── _config.yml ├── inst ├── blank.html └── paperFigs │ ├── Fig1.R │ └── v1_Fig1.R ├── man ├── CalcAllSCV.Rd ├── CalcCGS.Rd ├── CalcDEcombn.Rd ├── CalcDEvsRest.Rd ├── CalcSCV.Rd ├── CalcSilhouette.Rd ├── ColNNZ.Rd ├── DEdist.Rd ├── DEdistNN.Rd ├── DEmarker.Rd ├── DEneighb.Rd ├── RowNNZ.Rd ├── addCellMarkersToCGS.Rd ├── cosineSim.Rd ├── dotplotDEgenes.Rd ├── findKeyType.Rd ├── fx_calcCGS.Rd ├── fx_calcCGS_BP.Rd ├── fx_calcDEcombn.Rd ├── fx_calcDEcombn_BP.Rd ├── fx_calcDEcombn_slow.Rd ├── fx_calcDEvsRest.Rd ├── fx_calcDEvsRest_BP.Rd ├── fx_calcDEvsRest_slow.Rd ├── fx_calcDist_cellEmb.Rd ├── fx_calcDist_geneExpr.Rd ├── fx_calcDist_numDE.Rd ├── fx_calcDist_scoreDE.Rd ├── fx_calcEScombn.Rd ├── fx_calcESvsRest.Rd ├── fx_calcESvsRest_BP.Rd ├── fx_calcMarker.Rd ├── fx_calcNeighb.Rd ├── fx_calcSilhouette.Rd ├── getEmb.Rd ├── getExpr.Rd ├── getMD.Rd ├── hasEmb.Rd ├── labelCellTypes.Rd ├── map2symbol.Rd ├── meanLogX.Rd ├── origin.label.dist.Rd ├── overlap.edge.Rd ├── overlap.proportion.point.Rd ├── plot_GEboxplot.Rd ├── plot_clustSep.Rd ├── plot_clusterGenes_DEgenes.Rd ├── plot_clusterGenes_markers.Rd ├── plot_clusterGenes_search.Rd ├── plot_compareClusts.Rd ├── plot_deDotplot.Rd ├── plot_mdCompare.Rd ├── plot_mdPerClust.Rd ├── plot_sil.Rd ├── plot_tsne.Rd ├── runShiny.Rd ├── sCVdata-class.Rd ├── sCVparams-class.Rd ├── scClustViz.Rd ├── spreadLabels2.Rd ├── subsetCells.Rd └── tsne_labels.Rd ├── scClustViz.Rproj └── tests ├── testthat.R └── testthat ├── test_CalcCGS.R ├── test_CalcDEcombn.R ├── test_CalcDEvsRest.R └── test_DEdist.R /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BaderLab/scClustViz/HEAD/.Rbuildignore 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