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Seurat  

Tools for Single Cell Genomics
View on CRAN: Click here


Download and install Seurat package within the R console
Install from CRAN:
install.packages("Seurat")

Install from Github:
library("remotes")
install_github("cran/Seurat")

Install by package version:
library("remotes")
install_version("Seurat", "5.1.0")



Attach the package and use:
library("Seurat")
Maintained by
Rahul Satija
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-08-22
Latest Update: 2024-02-29
Description:
A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details.
How to cite:
Rahul Satija (2017). Seurat: Tools for Single Cell Genomics. R package version 5.1.0, https://cran.r-project.org/web/packages/Seurat. Accessed 07 Nov. 2024.
Previous versions and publish date:
2.0.1 (2017-08-22 16:57), 2.1.0 (2017-10-12 22:36), 2.2.0 (2018-01-10 22:46), 2.2.1 (2018-02-14 20:53), 2.3.0 (2018-03-23 09:49), 2.3.1 (2018-05-05 08:29), 2.3.2 (2018-06-12 18:09), 2.3.3 (2018-07-03 00:10), 2.3.4 (2018-07-20 10:14), 3.0.0 (2019-04-15 23:54), 3.0.1 (2019-05-16 18:21), 3.0.2 (2019-06-15 00:33), 3.1.0 (2019-08-20 23:40), 3.1.1 (2019-10-03 14:40), 3.1.2 (2019-12-12 23:20), 3.1.3 (2020-02-11 22:40), 3.1.4 (2020-02-26 20:00), 3.1.5 (2020-04-16 13:50), 3.2.0 (2020-07-16 06:30), 3.2.1 (2020-09-07 12:20), 3.2.2 (2020-09-26 06:30), 3.2.3 (2020-12-15 11:10), 4.0.0 (2021-01-30 01:00), 4.0.1 (2021-03-18 07:30), 4.0.2 (2021-05-21 00:00), 4.0.3 (2021-06-10 23:20), 4.0.4 (2021-08-20 21:10), 4.0.5 (2021-10-17 22:30), 4.0.6 (2021-12-16 18:00), 4.1.0 (2022-01-14 19:32), 4.1.1 (2022-05-02 07:40), 4.2.0 (2022-09-22 00:50), 4.2.1 (2022-11-08 01:00), 4.3.0.1 (2023-06-22 09:04), 4.3.0 (2022-11-19 00:30), 4.4.0 (2023-09-28 10:50), 5.0.0 (2023-11-04 06:30), 5.0.1 (2023-11-18 00:10), 5.0.2 (2024-02-29 01:20), 5.0.3 (2024-03-19 00:40)
Other packages that cited Seurat R package
View Seurat citation profile
Other R packages that Seurat depends, imports, suggests or enhances
Complete documentation for Seurat
Functions, R codes and Examples using the Seurat R package
Some associated functions: AddAzimuthResults . AddAzimuthScores . AddModuleScore . AggregateExpression . AnchorSet-class . AnnotateAnchors . Assay-class . AugmentPlot . AutoPointSize . AverageExpression . BGTextColor . BarcodeInflectionsPlot . BuildClusterTree . CalcPerturbSig . CalculateBarcodeInflections . CaseMatch . CellCycleScoring . CellScatter . CellSelector . Cells . CellsByImage . CollapseEmbeddingOutliers . CollapseSpeciesExpressionMatrix . ColorDimSplit . CombinePlots . CreateSCTAssayObject . CustomDistance . CustomPalette . DEenrichRPlot . DietSeurat . DimHeatmap . DimPlot . DimReduc-class . DiscretePalette . DoHeatmap . DotPlot . ElbowPlot . ExpMean . ExpSD . ExpVar . FastRowScale . FeaturePlot . FeatureScatter . FilterSlideSeq . FindAllMarkers . FindClusters . FindConservedMarkers . FindIntegrationAnchors . FindMarkers . FindMultiModalNeighbors . FindNeighbors . FindSpatiallyVariableFeatures . FindSubCluster . FindTransferAnchors . FindVariableFeatures . FoldChange . GetAssay . GetImage . GetIntegrationData . GetResidual . GetTissueCoordinates . GetTransferPredictions . Graph-class . GroupCorrelation . GroupCorrelationPlot . HTODemux . HTOHeatmap . HVFInfo.SCTAssay . HoverLocator . IFeaturePlot . ISpatialDimPlot . ISpatialFeaturePlot . ImageDimPlot . ImageFeaturePlot . IntegrateData . IntegrateEmbeddings . IntegrationAnchorSet-class . IntegrationData-class . JackStraw . JackStrawData-class . JackStrawPlot . L2CCA . L2Dim . LabelClusters . LabelPoints . LinkedPlots . Load10X_Spatial . LoadAnnoyIndex . LoadSTARmap . LocalStruct . LogNormalize . LogVMR . MULTIseqDemux . MapQuery . MappingScore . MetaFeature . MinMax . MixingMetric . MixscapeHeatmap . MixscapeLDA . ModalityWeights-class . NNPlot . Neighbor-class . NormalizeData . PCASigGenes . PercentAbove . PercentageFeatureSet . PlotClusterTree . PlotPerturbScore . PolyDimPlot . PolyFeaturePlot . PredictAssay . PrepLDA . PrepSCTFindMarkers . PrepSCTIntegration . ProjectDim . ProjectUMAP . Radius . Read10X . Read10X_Image . Read10X_h5 . ReadAkoya . ReadMtx . ReadNanostring . ReadParseBio . ReadSTARsolo . ReadSlideSeq . ReadVitessce . ReadVizgen . ReadXenium . RegroupIdents . RelativeCounts . RenameCells . RidgePlot . RunCCA . RunICA . RunLDA . RunMarkVario . RunMixscape . RunMoransI . RunPCA . RunSLSI . RunSPCA . RunTSNE . RunUMAP . SCTAssay-class . SCTResults . SCTransform . STARmap-class . SampleUMI . SaveAnnoyIndex . ScaleData . ScaleFactors . ScoreJackStraw . SelectIntegrationFeatures . SetIntegrationData . SetQuantile . Seurat-class . Seurat-package . SeuratCommand-class . SeuratTheme . SingleCorPlot . SingleDimPlot . SingleExIPlot . SingleImageMap . SingleImagePlot . SingleRasterMap . SingleSpatialPlot . SlideSeq-class . SpatialImage-class . SpatialPlot . SplitObject . SubsetByBarcodeInflections . TopCells . TopFeatures . TopNeighbors . TransferAnchorSet-class . TransferData . UpdateSCTAssays . UpdateSymbolList . VariableFeaturePlot . VisiumV1-class . VizDimLoadings . VlnPlot . as.CellDataSet . as.Seurat . as.SingleCellExperiment . as.sparse . cc.genes . cc.genes.updated.2019 . contrast-theory . fortify-Spatial . merge.SCTAssay . reexports . subset.AnchorSet . 
Some associated R codes: RcppExports.R . clustering.R . convenience.R . data.R . differential_expression.R . dimensional_reduction.R . generics.R . integration.R . mixscape.R . objects.R . preprocessing.R . reexports.R . tree.R . utilities.R . visualization.R . zzz.R .  Full Seurat package functions and examples
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