Files in Seurat
Tools for Single Cell Genomics

MD5
NEWS.md README.md
NAMESPACE
DESCRIPTION
LICENSE
R/RcppExports.R R/preprocessing.R R/visualization.R R/utilities.R R/data.R R/clustering.R R/convenience.R R/integration.R R/differential_expression.R R/generics.R R/objects.R R/tree.R R/zzz.R R/dimensional_reduction.R
src/Makevars
src/ModularityOptimizer.h
src/integration.h
src/RcppExports.cpp
src/integration.cpp
src/snn.cpp
src/ModularityOptimizer.cpp
src/RModularityOptimizer.cpp
src/data_manipulation.h
src/valid_pointer.c
src/data_manipulation.cpp
src/snn.h
inst/CITATION
inst/extdata/pbmc_raw.txt
tests/testthat.R
tests/testdata/matrix.mtx
tests/testdata/genes.tsv
tests/testdata/barcodes.tsv
tests/testdata/nbt_small.Rdata
tests/testdata/cr3.0/features.tsv.gz
tests/testdata/cr3.0/barcodes.tsv.gz
tests/testdata/cr3.0/matrix.mtx.gz
tests/testdata/visium/filtered_feature_bc_matrix.h5
tests/testdata/visium/spatial/scalefactors_json.json
tests/testdata/visium/spatial/tissue_positions_list.csv
tests/testdata/visium/spatial/tissue_lowres_image.png
tests/testthat/test_data_manipulation.R tests/testthat/test_preprocessing.R tests/testthat/test_utilities.R tests/testthat/test_modularity_optimizer.R tests/testthat/test_load_10X.R tests/testthat/test_differential_expression.R tests/testthat/test_dimensional_reduction.R tests/testthat/test_objects.R tests/testthat/test_visualization.R
data/pbmc_small.rda
data/cc.genes.rda
data/cc.genes.updated.2019.rda
man/as.Graph.Rd man/FindAllMarkers.Rd man/SlideSeq-class.Rd man/IntegrationData-class.Rd man/FilterSlideSeq.Rd man/CreateGeneActivityMatrix.Rd man/UpdateSymbolList.Rd man/contrast-theory.Rd man/Loadings.Rd man/PrepSCTIntegration.Rd man/Neighbor-class.Rd man/ALRAChooseKPlot.Rd man/FindNeighbors.Rd man/ExpVar.Rd man/SubsetData.Rd man/LoadSTARmap.Rd man/VizDimLoadings.Rd man/SelectIntegrationFeatures.Rd man/print.DimReduc.Rd man/SaveAnnoyIndex.Rd man/DimReduc-class.Rd man/as.CellDataSet.Rd man/MetaFeature.Rd man/CollapseSpeciesExpressionMatrix.Rd man/Project.Rd man/LocalStruct.Rd man/ExpMean.Rd man/LogNormalize.Rd man/CalculateBarcodeInflections.Rd man/DiscretePalette.Rd man/RidgePlot.Rd man/L2Dim.Rd man/UpdateSeuratObject.Rd man/LabelPoints.Rd man/Embeddings.Rd man/ReadSlideSeq.Rd man/SplitObject.Rd man/RunMoransI.Rd man/Distances.Rd man/PercentageFeatureSet.Rd man/HoverLocator.Rd man/Cells.Rd man/GetTissueCoordinates.Rd man/ExportToCellbrowser.Rd man/SetIntegrationData.Rd man/Read10X_h5.Rd man/RowMergeSparseMatrices.Rd man/FeaturePlot.Rd man/Assay-class.Rd man/Radius.Rd man/Key.Rd man/SVFInfo.Rd man/FindMarkers.Rd man/VariableFeatures.Rd man/SpatialImage-class.Rd man/SpatialPlot.Rd man/Tool.Rd man/GetTransferPredictions.Rd man/oldseurat-class.Rd man/Load10X_Spatial.Rd man/Reductions.Rd man/CellsByImage.Rd man/Misc.Rd man/GroupCorrelationPlot.Rd man/RenameCells.Rd man/ScoreJackStraw.Rd man/HTOHeatmap.Rd man/DefaultAssay.Rd man/Neighbors.Rd man/RunICA.Rd man/SeuratCommand-class.Rd man/CaseMatch.Rd man/FindSpatiallyVariableFeatures.Rd man/BGTextColor.Rd man/as.Neighbor.Rd man/cc.genes.Rd man/ElbowPlot.Rd man/ISpatialDimPlot.Rd man/DotPlot.Rd man/RunCCA.Rd man/cc.genes.updated.2019.Rd man/FindClusters.Rd man/IsGlobal.Rd man/pbmc_small.Rd man/as.list.SeuratCommand.Rd man/GetAssay.Rd man/CombinePlots.Rd man/SetAssayData.Rd man/MULTIseqDemux.Rd man/BarcodeInflectionsPlot.Rd man/Index.Rd man/FindTransferAnchors.Rd man/NormalizeData.Rd man/Command.Rd man/LinkedPlots.Rd man/PolyFeaturePlot.Rd man/GroupCorrelation.Rd man/SCTransform.Rd man/SeuratTheme.Rd man/JackStrawData-class.Rd man/CellScatter.Rd man/DimHeatmap.Rd man/CellsByIdentities.Rd man/WhichCells.Rd man/Images.Rd man/ExpSD.Rd man/AddMetaData.Rd man/SubsetByBarcodeInflections.Rd man/VlnPlot.Rd man/as.loom.Rd man/Idents.Rd man/Indices.Rd man/Read10X.Rd man/TF.IDF.Rd man/Seurat-package.Rd man/RunMarkVario.Rd man/JackStraw.Rd man/GetResidual.Rd man/RelativeCounts.Rd man/FeatureScatter.Rd man/JackStrawPlot.Rd man/as.Seurat.Rd man/DoHeatmap.Rd man/FastRowScale.Rd man/AverageExpression.Rd man/LoadAnnoyIndex.Rd man/PolyDimPlot.Rd man/LogVMR.Rd man/RunTSNE.Rd man/STARmap-class.Rd man/FindVariableFeatures.Rd man/LabelClusters.Rd man/CustomDistance.Rd man/L2CCA.Rd man/Assays.Rd man/as.sparse.Rd man/CreateAssayObject.Rd man/RunUMAP.Rd man/PlotClusterTree.Rd man/PCASigGenes.Rd man/ScaleData.Rd man/CollapseEmbeddingOutliers.Rd man/TopNeighbors.Rd man/RunALRA.Rd man/ReadAlevinCsv.Rd man/Stdev.Rd man/TransferData.Rd man/CreateDimReducObject.Rd man/as.SingleCellExperiment.Rd man/Graph-class.Rd man/HVFInfo.Rd man/subset.Seurat.Rd man/MinMax.Rd man/Read10X_Image.Rd man/ProjectDim.Rd man/TopCells.Rd man/SpatiallyVariableFeatures.Rd man/RenameAssays.Rd man/DietSeurat.Rd man/TopFeatures.Rd man/OldWhichCells.Rd man/Seurat-class.Rd man/RegroupIdents.Rd man/MixingMetric.Rd man/VisiumV1-class.Rd man/LogSeuratCommand.Rd man/GetIntegrationData.Rd man/RunLSI.Rd man/StopCellbrowser.Rd man/ColorDimSplit.Rd man/FindIntegrationAnchors.Rd man/DimPlot.Rd man/IFeaturePlot.Rd man/GetAssayData.Rd man/VariableFeaturePlot.Rd man/ReadAlevin.Rd man/AugmentPlot.Rd man/FindConservedMarkers.Rd man/HTODemux.Rd man/JS.Rd man/CellCycleScoring.Rd man/GetImage.Rd man/RunPCA.Rd man/merge.Seurat.Rd man/CustomPalette.Rd man/SampleUMI.Rd man/ScaleFactors.Rd man/AnchorSet-class.Rd man/FetchData.Rd man/ISpatialFeaturePlot.Rd man/CreateSeuratObject.Rd man/BuildClusterTree.Rd man/AddModuleScore.Rd man/IntegrateData.Rd man/CellSelector.Rd man/h5ad.Rd
Seurat documentation built on Jan. 13, 2021, 7:11 p.m.