Files in satijalab/seurat

Tools for Single Cell Genomics

.Rbuildignore

.gitattributes

.github/ISSUE_TEMPLATE/analysis-question.md .github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/documentation.md .github/ISSUE_TEMPLATE/feature-request.md

.github/no-response.yml

.github/pull_request_template.md

.github/workflows/R_CMD_check.yaml

.gitignore

.travis.yml

CODE_OF_CONDUCT.md

DESCRIPTION

LICENSE

LICENSE.md

NAMESPACE

NEWS.md R/RcppExports.R R/clustering.R R/convenience.R R/data.R R/differential_expression.R R/dimensional_reduction.R R/generics.R R/integration.R R/integration5.R R/mixscape.R R/objects.R R/preprocessing.R R/preprocessing5.R R/reexports.R R/roxygen.R R/sketching.R R/tree.R R/utilities.R R/visualization.R

R/zfRenderSeurat.old

R/zzz.R README.md

_pkgdown.yaml

appveyor.yml

azure-pipelines.yml

cran-comments.md

data/cc.genes.rda

data/cc.genes.updated.2019.rda

index.md

inst/CITATION

inst/extdata/pbmc_raw.txt

man/AddAzimuthResults.Rd man/AddAzimuthScores.Rd man/AddModuleScore.Rd man/AggregateExpression.Rd man/AnchorSet-class.Rd man/AnnotateAnchors.Rd man/Assay-class.Rd man/AugmentPlot.Rd man/AutoPointSize.Rd man/AverageExpression.Rd man/BGTextColor.Rd man/BarcodeInflectionsPlot.Rd man/BridgeCellsRepresentation.Rd man/BridgeReferenceSet-class.Rd man/BuildClusterTree.Rd man/BuildNicheAssay.Rd man/CCAIntegration.Rd man/CalcDispersion.Rd man/CalcPerturbSig.Rd man/CalculateBarcodeInflections.Rd man/CaseMatch.Rd man/CellCycleScoring.Rd man/CellScatter.Rd man/CellSelector.Rd man/Cells.Rd man/CellsByImage.Rd man/CollapseEmbeddingOutliers.Rd man/CollapseSpeciesExpressionMatrix.Rd man/ColorDimSplit.Rd man/CombinePlots.Rd man/CountSketch.Rd man/CreateCategoryMatrix.Rd man/CreateSCTAssayObject.Rd man/CustomDistance.Rd man/CustomPalette.Rd man/DEenrichRPlot.Rd man/DISP.Rd man/DietSeurat.Rd man/DimHeatmap.Rd man/DimPlot.Rd man/DimReduc-class.Rd man/DiscretePalette.Rd man/DoHeatmap.Rd man/DotPlot.Rd man/ElbowPlot.Rd man/ExpMean.Rd man/ExpSD.Rd man/ExpVar.Rd man/FastRPCAIntegration.Rd man/FastRowScale.Rd man/FeaturePlot.Rd man/FeatureScatter.Rd man/FetchResidualSCTModel.Rd man/FetchResiduals.Rd man/FetchResiduals_reference.Rd man/FilterSlideSeq.Rd man/FindAllMarkers.Rd man/FindBridgeAnchor.Rd man/FindBridgeIntegrationAnchors.Rd man/FindBridgeTransferAnchors.Rd man/FindClusters.Rd man/FindConservedMarkers.Rd man/FindIntegrationAnchors.Rd man/FindMarkers.Rd man/FindMultiModalNeighbors.Rd man/FindNeighbors.Rd man/FindSpatiallyVariableFeatures.Rd man/FindSubCluster.Rd man/FindTransferAnchors.Rd man/FindVariableFeatures.Rd man/FoldChange.Rd man/GaussianSketch.Rd man/GetAssay.Rd man/GetImage.Rd man/GetIntegrationData.Rd man/GetResidual.Rd man/GetTissueCoordinates.Rd man/GetTransferPredictions.Rd man/Graph-class.Rd man/GroupCorrelation.Rd man/GroupCorrelationPlot.Rd man/HTODemux.Rd man/HTOHeatmap.Rd man/HVFInfo.SCTAssay.Rd man/HarmonyIntegration.Rd man/HoverLocator.Rd man/IFeaturePlot.Rd man/ISpatialDimPlot.Rd man/ISpatialFeaturePlot.Rd man/ImageDimPlot.Rd man/ImageFeaturePlot.Rd man/IntegrateData.Rd man/IntegrateEmbeddings.Rd man/IntegrateLayers.Rd man/IntegrationAnchorSet-class.Rd man/IntegrationData-class.Rd man/JackStraw.Rd man/JackStrawData-class.Rd man/JackStrawPlot.Rd man/JointPCAIntegration.Rd man/L2CCA.Rd man/L2Dim.Rd man/LabelClusters.Rd man/LabelPoints.Rd man/LeverageScore.Rd man/LinkedPlots.Rd man/Load10X_Spatial.Rd man/LoadAnnoyIndex.Rd man/LoadCurioSeeker.Rd man/LoadSTARmap.Rd man/LocalStruct.Rd man/LogNormalize.Rd man/LogVMR.Rd man/MULTIseqDemux.Rd man/MVP.Rd man/MapQuery.Rd man/MappingScore.Rd man/MetaFeature.Rd man/MinMax.Rd man/MixingMetric.Rd man/MixscapeHeatmap.Rd man/MixscapeLDA.Rd man/ModalityWeights-class.Rd man/NNPlot.Rd man/NNtoGraph.Rd man/Neighbor-class.Rd man/NormalizeData.Rd man/PCASigGenes.Rd man/PercentAbove.Rd man/PercentageFeatureSet.Rd man/PlotClusterTree.Rd man/PlotPerturbScore.Rd man/PolyDimPlot.Rd man/PolyFeaturePlot.Rd man/PredictAssay.Rd man/PrepLDA.Rd man/PrepSCTFindMarkers.Rd man/PrepSCTIntegration.Rd man/PrepareBridgeReference.Rd man/ProjectCellEmbeddings.Rd man/ProjectData.Rd man/ProjectDim.Rd man/ProjectDimReduc.Rd man/ProjectIntegration.Rd man/ProjectUMAP.Rd man/PseudobulkExpression.Rd man/RPCAIntegration.Rd man/Radius.Rd man/Read10X.Rd man/Read10X_Image.Rd man/Read10X_h5.Rd man/Read10X_probe_metadata.Rd man/ReadAkoya.Rd man/ReadMtx.Rd man/ReadNanostring.Rd man/ReadParseBio.Rd man/ReadSTARsolo.Rd man/ReadSlideSeq.Rd man/ReadVitessce.Rd man/ReadVizgen.Rd man/ReadXenium.Rd man/RegroupIdents.Rd man/RelativeCounts.Rd man/RenameCells.Rd man/RidgePlot.Rd man/RunCCA.Rd man/RunGraphLaplacian.Rd man/RunICA.Rd man/RunLDA.Rd man/RunMarkVario.Rd man/RunMixscape.Rd man/RunMoransI.Rd man/RunPCA.Rd man/RunSLSI.Rd man/RunSPCA.Rd man/RunTSNE.Rd man/RunUMAP.Rd man/SCTAssay-class.Rd man/SCTResults.Rd man/SCTransform.Rd man/STARmap-class.Rd man/SampleUMI.Rd man/SaveAnnoyIndex.Rd man/ScaleData.Rd man/ScaleFactors.Rd man/ScoreJackStraw.Rd man/SelectIntegrationFeatures.Rd man/SelectIntegrationFeatures5.Rd man/SelectSCTIntegrationFeatures.Rd man/SetIntegrationData.Rd man/SetQuantile.Rd man/Seurat-class.Rd man/Seurat-package.Rd man/SeuratCommand-class.Rd man/SeuratTheme.Rd man/SingleCorPlot.Rd man/SingleDimPlot.Rd man/SingleExIPlot.Rd man/SingleImageMap.Rd man/SingleImagePlot.Rd man/SingleRasterMap.Rd man/SingleSpatialPlot.Rd man/SketchData.Rd man/SlideSeq-class.Rd man/SpatialImage-class.Rd man/SpatialPlot.Rd man/SplitObject.Rd man/SubsetByBarcodeInflections.Rd man/TopCells.Rd man/TopFeatures.Rd man/TopNeighbors.Rd man/TransferAnchorSet-class.Rd man/TransferData.Rd man/TransferSketchLabels.Rd man/UnSketchEmbeddings.Rd man/UpdateSCTAssays.Rd man/UpdateSymbolList.Rd man/VST.Rd man/VariableFeaturePlot.Rd man/VisiumV1-class.Rd man/VizDimLoadings.Rd man/VlnPlot.Rd man/as.CellDataSet.Rd man/as.Seurat.Rd man/as.SingleCellExperiment.Rd man/as.sparse.Rd man/cc.genes.Rd man/cc.genes.updated.2019.Rd man/contrast-theory.Rd man/fortify-Spatial.Rd man/merge.SCTAssay.Rd man/reexports.Rd man/roxygen/templates/note-reqdpkg.R man/roxygen/templates/param-dotsi.R man/roxygen/templates/param-dotsm.R man/roxygen/templates/section-future.R man/roxygen/templates/section-progressr.R man/roxygen/templates/seealso-methods.R man/subset.AnchorSet.Rd man/writing-integration.Rd

seurat.Rproj

src/Makevars

src/ModularityOptimizer.cpp

src/ModularityOptimizer.h

src/RModularityOptimizer.cpp

src/RcppExports.cpp

src/data_manipulation.cpp

src/data_manipulation.h

src/fast_NN_dist.cpp

src/integration.cpp

src/integration.h

src/snn.cpp

src/snn.h

src/stats.cpp

src/valid_pointer.c

tests/testdata/barcodes.tsv

tests/testdata/cr3.0/barcodes.tsv.gz

tests/testdata/cr3.0/features.tsv.gz

tests/testdata/cr3.0/matrix.mtx.gz

tests/testdata/genes.tsv

tests/testdata/matrix.mtx

tests/testdata/nbt_small.Rdata

tests/testdata/visium/filtered_feature_bc_matrix.h5

tests/testdata/visium/raw_probe_bc_matrix.h5

tests/testdata/visium/spatial/scalefactors_json.json

tests/testdata/visium/spatial/tissue_lowres_image.png

tests/testdata/visium/spatial/tissue_positions_list.csv

tests/testthat.R tests/testthat/test_data_manipulation.R tests/testthat/test_differential_expression.R tests/testthat/test_dimensional_reduction.R tests/testthat/test_integratedata.R tests/testthat/test_integration.R tests/testthat/test_integration5.R tests/testthat/test_load_10X.R tests/testthat/test_modularity_optimizer.R tests/testthat/test_objects.R tests/testthat/test_preprocessing.R tests/testthat/test_read_mtx.R tests/testthat/test_transferdata.R tests/testthat/test_utilities.R tests/testthat/test_visualization.R

travis_setup.sh

vignettes/COVID_SCTMapping.Rmd vignettes/ParseBio_sketch_integration.Rmd vignettes/announcements.Rmd vignettes/archive.Rmd

vignettes/archive.yaml

vignettes/assets/anchorsb_2018.png

vignettes/assets/conversion_vignette.png

vignettes/assets/de_vignette.png

vignettes/assets/future_rocket.png

vignettes/assets/hashing_vignette.png

vignettes/assets/pbmc_dcs_cells.txt

vignettes/assets/pbmc_select.gif

vignettes/assets/sctransform.png

vignettes/assets/sctransform_v2.png

vignettes/assets/seurat_banner.jpg

vignettes/atacseq_integration_vignette.Rmd vignettes/cell_cycle_vignette.Rmd vignettes/conversion_vignette.Rmd vignettes/de_vignette.Rmd vignettes/dim_reduction_vignette.Rmd vignettes/essential_commands.Rmd vignettes/extensions.Rmd vignettes/future_vignette.Rmd vignettes/get_started.Rmd vignettes/get_started_v5.Rmd vignettes/get_started_v5_new.Rmd vignettes/hashing_vignette.Rmd vignettes/install.Rmd vignettes/install_v5.Rmd vignettes/integration_introduction.Rmd vignettes/integration_large_datasets.Rmd vignettes/integration_mapping.Rmd vignettes/integration_rpca.Rmd vignettes/interaction_vignette.Rmd vignettes/merge_vignette.Rmd vignettes/mixscape_vignette.Rmd vignettes/multimodal_reference_mapping.Rmd vignettes/multimodal_vignette.Rmd

vignettes/pancreas_integrated_umap.jpg

vignettes/pbmc3k_tutorial.Rmd vignettes/sctransform_v2_vignette.Rmd vignettes/sctransform_vignette.Rmd vignettes/seurat5_archive.Rmd vignettes/seurat5_atacseq_integration_vignette.Rmd vignettes/seurat5_bpcells_interaction_vignette.Rmd vignettes/seurat5_cell_cycle_vignette.Rmd vignettes/seurat5_conversion_vignette.Rmd vignettes/seurat5_de_vignette.Rmd vignettes/seurat5_dim_reduction_vignette.Rmd vignettes/seurat5_essential_commands.Rmd vignettes/seurat5_extensions.Rmd vignettes/seurat5_future_vignette.Rmd vignettes/seurat5_get_started.Rmd vignettes/seurat5_hashing_vignette.Rmd vignettes/seurat5_integration.Rmd vignettes/seurat5_integration_bridge.Rmd vignettes/seurat5_integration_introduction.Rmd vignettes/seurat5_integration_large_datasets.Rmd vignettes/seurat5_integration_mapping.Rmd vignettes/seurat5_integration_rpca.Rmd vignettes/seurat5_interaction_vignette.Rmd vignettes/seurat5_merge_vignette.Rmd vignettes/seurat5_mixscape_vignette.Rmd vignettes/seurat5_multimodal_reference_mapping.Rmd vignettes/seurat5_multimodal_vignette.Rmd vignettes/seurat5_pbmc3k_tutorial.Rmd vignettes/seurat5_sctransform_integration.Rmd vignettes/seurat5_sctransform_v2_vignette.Rmd vignettes/seurat5_sctransform_vignette.Rmd vignettes/seurat5_sketch_analysis.Rmd vignettes/seurat5_spatial_vignette.Rmd vignettes/seurat5_spatial_vignette_2.Rmd vignettes/seurat5_v4_changes.Rmd vignettes/seurat5_visualization_vignette.Rmd vignettes/seurat5_weighted_nearest_neighbor_analysis.Rmd vignettes/spatial_vignette.Rmd vignettes/spatial_vignette_2.Rmd vignettes/v4_changes.Rmd

vignettes/vignettes.yaml

vignettes/vignettes_v5.yaml

vignettes/vignettes_v5_new.yaml

vignettes/visualization_vignette.Rmd vignettes/weighted_nearest_neighbor_analysis.Rmd

satijalab/seurat documentation built on March 20, 2024, 8:41 p.m.