Files in mayer-lab/SeuratForMayer2018

Seurat : R Toolkit for Single Cell Genomics

R/RcppExports.R R/cluster_determination.R R/cluster_determination_internal.R R/cluster_validation.R R/deprecated_functions.R R/differential_expression.R R/differential_expression_internal.R R/dimensional_reduction.R R/dimensional_reduction_internal.R R/dimensional_reduction_utilities.R R/interaction.R R/jackstraw.R R/jackstraw_internal.R R/multi_modal.R R/plotting.R R/plotting_internal.R R/plotting_utilities.R R/preprocessing.R R/preprocessing_internal.R R/printing_utilities.R R/scoring.R R/seurat.R R/snn.R R/spatial.R R/spatial_internal.R R/tSNE_project.R R/utilities.R R/utilities_internal.R R/zfRenderSeurat.R README.md man/AddImputedScore.Rd man/AddMetaData.Rd man/AddModuleScore.Rd man/AddSamples.Rd man/AddSmoothedScore.Rd man/AlignSubspace.Rd man/AssessNodes.Rd man/AssessSplit.Rd man/AverageDetectionRate.Rd man/AverageExpression.Rd man/AveragePCA.Rd man/BlackAndWhite.Rd man/BuildClusterTree.Rd man/BuildRFClassifier.Rd man/BuildSNN.Rd man/CalcVarExpRatio.Rd man/CaseMatch.Rd man/CellCycleScoring.Rd man/CellPlot.Rd man/ClassifyCells.Rd man/ColorTSNESplit.Rd man/CreateSeuratObject.Rd man/CustomDistance.Rd man/CustomPalette.Rd man/DBClustDimension.Rd man/DMEmbed.Rd man/DMLoad.Rd man/DMPlot.Rd man/DarkTheme.Rd man/DiffExpTest.Rd man/DiffTTest.Rd man/DimElbowPlot.Rd man/DimHeatmap.Rd man/DimPlot.Rd man/DimTopCells.Rd man/DimTopGenes.Rd man/DoHeatmap.Rd man/DoKMeans.Rd man/DotPlot.Rd man/DotPlotOld.Rd man/ExpMean.Rd man/ExpSD.Rd man/ExpVar.Rd man/ExtractField.Rd man/FastWhichCells.Rd man/FeatureHeatmap.Rd man/FeatureLocator.Rd man/FeaturePlot.Rd man/FetchData.Rd man/FilterCells.Rd man/FindAllMarkers.Rd man/FindAllMarkersNode.Rd man/FindClusters.Rd man/FindConservedMarkers.Rd man/FindMarkers.Rd man/FindMarkersNode.Rd man/FindVariableGenes.Rd man/FitGeneK.Rd man/GenePlot.Rd man/GenesInCluster.Rd man/GetAssayData.Rd man/GetCellEmbeddings.Rd man/GetCentroids.Rd man/GetClusters.Rd man/GetDimReduction.Rd man/GetGeneLoadings.Rd man/HoverLocator.Rd man/ICAEmbed.Rd man/ICALoad.Rd man/ICAPlot.Rd man/ICHeatmap.Rd man/ICTopCells.Rd man/ICTopGenes.Rd man/InitialMapping.Rd man/JackStraw.Rd man/JackStrawPlot.Rd man/JoyPlot.Rd man/KClustDimension.Rd man/KMeansHeatmap.Rd man/LogNormalize.Rd man/LogVMR.Rd man/MakeSparse.Rd man/MarkerTest.Rd man/MatrixRowShuffle.Rd man/MergeNode.Rd man/MergeSeurat.Rd man/MinMax.Rd man/MultiModal_CCA.Rd man/NegBinomDETest.Rd man/NegBinomRegDETest.Rd man/NodeHeatmap.Rd man/NormalizeData.Rd man/NumberClusters.Rd man/OldDoHeatmap.Rd man/PCAEmbed.Rd man/PCALoad.Rd man/PCAPlot.Rd man/PCASigGenes.Rd man/PCElbowPlot.Rd man/PCHeatmap.Rd man/PCTopCells.Rd man/PCTopGenes.Rd man/PlotClusterTree.Rd man/PoissonDETest.Rd man/PosteriorPlot.Rd man/PrintAlignSubspaceParams.Rd man/PrintCCAParams.Rd man/PrintCalcParams.Rd man/PrintCalcVarExpRatioParams.Rd man/PrintDMParams.Rd man/PrintDim.Rd man/PrintFindClustersParams.Rd man/PrintICA.Rd man/PrintICAParams.Rd man/PrintPCA.Rd man/PrintPCAParams.Rd man/PrintSNNParams.Rd man/PrintTSNEParams.Rd man/ProjectDim.Rd man/ProjectPCA.Rd man/PurpleAndYellow.Rd man/Read10X.Rd man/RefinedMapping.Rd man/RegressOutResid.Rd man/RemoveFromTable.Rd man/RenameIdent.Rd man/ReorderIdent.Rd man/RunCCA.Rd man/RunDiffusion.Rd man/RunICA.Rd man/RunPCA.Rd man/RunTSNE.Rd man/SampleUMI.Rd man/SaveClusters.Rd man/ScaleData.Rd man/ScaleDataR.Rd man/SetAllIdent.Rd man/SetAssayData.Rd man/SetClusters.Rd man/SetDimReduction.Rd man/SetIdent.Rd man/Seurat-deprecated.Rd man/Shuffle.Rd man/SplitDotPlotGG.Rd man/StashIdent.Rd man/SubsetColumn.Rd man/SubsetData.Rd man/SubsetRow.Rd man/TSNEPlot.Rd man/TobitTest.Rd man/UpdateSeuratObject.Rd man/ValidateClusters.Rd man/ValidateSpecificClusters.Rd man/VariableGenePlot.Rd man/VizClassification.Rd man/VizDimReduction.Rd man/VizICA.Rd man/VizPCA.Rd man/VlnPlot.Rd man/WhichCells.Rd man/seurat.Rd man/show-methods.Rd man/zfRenderSeurat.Rd tests/testthat.R tests/testthat/test_data_manipulation.R tests/testthat/test_seurat_object.R