Package: Seurat 4.4.0

Paul Hoffman

Seurat: Tools for Single Cell Genomics

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) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Authors:Andrew Butler [ctb], Saket Choudhary [ctb], Charlotte Darby [ctb], Jeff Farrell [ctb], Christoph Hafemeister [ctb], Yuhan Hao [ctb], Austin Hartman [ctb], Paul Hoffman [aut, cre], Jaison Jain [ctb], Madeline Kowalski [ctb], Efthymia Papalexi [ctb], Patrick Roelli [ctb], Rahul Satija [ctb], Karthik Shekhar [ctb], Avi Srivastava [ctb], Tim Stuart [ctb], Kristof Torkenczy [ctb], Shiwei Zheng [ctb], Satija Lab and Collaborators [fnd]

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NEWS

# Install 'Seurat' in R:

install.packages('Seurat', repos = c('https://satijalab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/satijalab/seurat/issues

Pkgdown site:https://satijalab.org

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

cc.genes - Cell cycle genes
cc.genes.updated.2019 - Cell cycle genes: 2019 update

On CRAN:

human-cell-atlas single-cell-genomics single-cell-rna-seq cpp

16.56 score 2.3k stars 68 packages 49k scripts 36k downloads 1.5k mentions 255 exports 143 dependencies

Last updated 1 years agofrom:74905f1be2 (on seurat4). Checks:1 OK, 8 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 10 2025
R-4.5-win-x86_64	WARNING	Jan 10 2025
R-4.5-linux-x86_64	WARNING	Jan 10 2025
R-4.4-win-x86_64	WARNING	Jan 10 2025
R-4.4-mac-x86_64	WARNING	Jan 10 2025
R-4.4-mac-aarch64	WARNING	Jan 10 2025
R-4.3-win-x86_64	WARNING	Jan 10 2025
R-4.3-mac-x86_64	WARNING	Jan 10 2025
R-4.3-mac-aarch64	WARNING	Jan 10 2025

Exports:%||%%iff%AddAzimuthResults AddMetaData AddModuleScore AggregateExpression AnnotateAnchors as.CellDataSet as.Graph as.Neighbor as.Seurat as.SingleCellExperiment as.sparse Assays AugmentPlot AutoPointSize AverageExpression BarcodeInflectionsPlot BGTextColor BlackAndWhite BlueAndRed BoldTitle BuildClusterTree CalcPerturbSig CalculateBarcodeInflections CaseMatch CellCycleScoring Cells CellsByIdentities CellScatter CellSelector CenterTitle CollapseEmbeddingOutliers CollapseSpeciesExpressionMatrix ColorDimSplit CombinePlots Command CreateAssayObject CreateDimReducObject CreateSCTAssayObject CreateSeuratObject CustomDistance CustomPalette DarkTheme DEenrichRPlot DefaultAssay DefaultAssay<-DietSeurat DimHeatmap DimPlot DiscretePalette Distances DoHeatmap DotPlot ElbowPlot Embeddings ExpMean ExpSD ExpVar FastRowScale FeatureLocator FeaturePlot FeatureScatter FetchData FilterSlideSeq FindAllMarkers FindClusters FindConservedMarkers FindIntegrationAnchors FindMarkers FindMultiModalNeighbors FindNeighbors FindSpatiallyVariableFeatures FindSubCluster FindTransferAnchors FindVariableFeatures FoldChange FontSize GeneSymbolThesarus GetAssay GetAssayData GetImage GetIntegrationData GetResidual GetTissueCoordinates GetTransferPredictions GroupCorrelation GroupCorrelationPlot HoverLocator HTODemux HTOHeatmap HVFInfo Idents Idents<-IFeaturePlot ImageDimPlot ImageFeaturePlot Images Index Index<-Indices IntegrateData IntegrateEmbeddings Intensity IsGlobal ISpatialDimPlot ISpatialFeaturePlot JackStraw JackStrawPlot JS JS<-Key Key<-L2CCA L2Dim LabelClusters LabelPoints LinkedDimPlot LinkedFeaturePlot Load10X_Spatial LoadAkoya LoadAnnoyIndex LoadCurioSeeker LoadHuBMAPCODEX Loadings Loadings<-LoadNanostring LoadSTARmap LoadVizgen LoadXenium LocalStruct LogNormalize LogSeuratCommand LogVMR Luminance MappingScore MapQuery MetaFeature MinMax Misc Misc<-MixingMetric MixscapeHeatmap MixscapeLDA MULTIseqDemux Neighbors NNPlot NoAxes NoGrid NoLegend NormalizeData PCAPlot PCASigGenes PCHeatmap PercentAbove PercentageFeatureSet PlotClusterTree PlotPerturbScore PolyDimPlot PolyFeaturePlot PredictAssay PrepLDA PrepSCTFindMarkers PrepSCTIntegration Project Project<-ProjectDim ProjectUMAP PurpleAndYellow Radius Read10X Read10X_h5 Read10X_Image Read10X_probe_metadata ReadAkoya ReadMtx ReadNanostring ReadParseBio ReadSlideSeq ReadSTARsolo ReadVitessce ReadVizgen ReadXenium Reductions RegroupIdents RelativeCounts RenameCells RenameIdents ReorderIdent RestoreLegend RidgePlot RotatedAxis RowMergeSparseMatrices RunCCA RunICA RunLDA RunMarkVario RunMixscape RunMoransI RunPCA RunSLSI RunSPCA RunTSNE RunUMAP SampleUMI SaveAnnoyIndex ScaleData scalefactors ScaleFactors ScoreJackStraw SCTransform SCTResults SCTResults<-SelectIntegrationFeatures SetAssayData SetIdent SetIntegrationData SetQuantile SeuratAxes SeuratTheme SingleCorPlot SingleDimPlot SingleExIPlot SingleImageMap SingleImagePlot SingleRasterMap SingleSpatialPlot SpatialDimPlot SpatialFeaturePlot SpatiallyVariableFeatures SpatialPlot SpatialTheme SplitObject StashIdent Stdev SubsetByBarcodeInflections SVFInfo Tool Tool<-TopCells TopFeatures TopNeighbors TransferData TSNEPlot UMAPPlot UpdateSCTAssays UpdateSeuratObject UpdateSymbolList VariableFeaturePlot VariableFeatures VariableFeatures<-VizDimLoadings VlnPlot WhichCells WhiteBackground

Dependencies:abind askpass base64enc BH bitops bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table deldir digest dotCall64 dplyr dqrng evaluate fansi farver fastmap fitdistrplus FNN fontawesome fs future future.apply generics ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval leiden lifecycle listenv lmtest magrittr MASS Matrix matrixStats memoise mgcv mime miniUI munsell nlme openssl parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne sass scales scattermore sctransform SeuratObject shiny sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable yaml zoo

Help page	Topics
Seurat: Tools for Single Cell Genomics	Seurat-package Seurat
Add Azimuth Results	AddAzimuthResults
Add Azimuth Scores	AddAzimuthScores
Calculate module scores for feature expression programs in single cells	AddModuleScore
Aggregated feature expression by identity class	AggregateExpression
The AnchorSet Class	AnchorSet AnchorSet-class
Add info to anchor matrix	AnnotateAnchors AnnotateAnchors.default AnnotateAnchors.IntegrationAnchorSet AnnotateAnchors.TransferAnchorSet
Convert objects to CellDataSet objects	as.CellDataSet as.CellDataSet.Seurat
Convert objects to 'Seurat' objects	as.Seurat.CellDataSet as.Seurat.SingleCellExperiment
Convert objects to SingleCellExperiment objects	as.SingleCellExperiment as.SingleCellExperiment.Seurat
Cast to Sparse	as.data.frame.Matrix as.sparse.H5Group
The Assay Class	Assay-class
Augments ggplot2-based plot with a PNG image.	AugmentPlot
Automagically calculate a point size for ggplot2-based scatter plots	AutoPointSize
Averaged feature expression by identity class	AverageExpression
Plot the Barcode Distribution and Calculated Inflection Points	BarcodeInflectionsPlot
Determine text color based on background color	BGTextColor
Create a custom color palette	BlackAndWhite BlueAndRed CustomPalette PurpleAndYellow
Phylogenetic Analysis of Identity Classes	BuildClusterTree
Calculate a perturbation Signature	CalcPerturbSig
Calculate the Barcode Distribution Inflection	CalculateBarcodeInflections
Match the case of character vectors	CaseMatch
Cell cycle genes	cc.genes
Cell cycle genes: 2019 update	cc.genes.updated.2019
Score cell cycle phases	CellCycleScoring
Get Cell Names	Cells.SCTModel Cells.SlideSeq Cells.STARmap Cells.VisiumV1
Get a vector of cell names associated with an image (or set of images)	CellsByImage
Cell-cell scatter plot	CellPlot CellScatter
Cell Selector	CellSelector FeatureLocator
Move outliers towards center on dimension reduction plot	CollapseEmbeddingOutliers
Slim down a multi-species expression matrix, when only one species is primarily of interenst.	CollapseSpeciesExpressionMatrix
Color dimensional reduction plot by tree split	ColorDimSplit
Combine ggplot2-based plots into a single plot	CombinePlots
Get the intensity and/or luminance of a color	contrast-theory Intensity Luminance
Create a SCT Assay object	CreateSCTAssayObject
Run a custom distance function on an input data matrix	CustomDistance
DE and EnrichR pathway visualization barplot	DEenrichRPlot
Slim down a Seurat object	DietSeurat
Dimensional reduction heatmap	DimHeatmap PCHeatmap
Dimensional reduction plot	DimPlot ICAPlot PCAPlot TSNEPlot UMAPPlot
The DimReduc Class	DimReduc-class
Discrete colour palettes from pals	DiscretePalette
Feature expression heatmap	DoHeatmap
Dot plot visualization	DotPlot SplitDotPlotGG
Quickly Pick Relevant Dimensions	ElbowPlot
Calculate the mean of logged values	ExpMean
Calculate the standard deviation of logged values	ExpSD
Calculate the variance of logged values	ExpVar
Scale and/or center matrix rowwise	FastRowScale
Visualize 'features' on a dimensional reduction plot	FeatureHeatmap FeaturePlot
Scatter plot of single cell data	FeatureScatter GenePlot
Filter stray beads from Slide-seq puck	FilterSlideSeq
Gene expression markers for all identity classes	FindAllMarkers FindAllMarkersNode
Cluster Determination	FindClusters FindClusters.default FindClusters.Seurat
Finds markers that are conserved between the groups	FindConservedMarkers
Find integration anchors	FindIntegrationAnchors
Gene expression markers of identity classes	FindMarkers FindMarkers.Assay FindMarkers.default FindMarkers.DimReduc FindMarkers.SCTAssay FindMarkers.Seurat FindMarkersNode
Construct weighted nearest neighbor graph	FindMultiModalNeighbors
(Shared) Nearest-neighbor graph construction	FindNeighbors FindNeighbors.Assay FindNeighbors.default FindNeighbors.dist FindNeighbors.Seurat
Find spatially variable features	FindSpatiallyVariableFeatures FindSpatiallyVariableFeatures.Assay FindSpatiallyVariableFeatures.default FindSpatiallyVariableFeatures.Seurat
Find subclusters under one cluster	FindSubCluster
Find transfer anchors	FindTransferAnchors
Find variable features	FindVariableFeatures FindVariableFeatures.Assay FindVariableFeatures.default FindVariableFeatures.SCTAssay FindVariableFeatures.Seurat FindVariableGenes
Fold Change	FoldChange FoldChange.Assay FoldChange.default FoldChange.DimReduc FoldChange.SCTAssay FoldChange.Seurat
Get an Assay object from a given Seurat object.	GetAssay GetAssay.Seurat
Get Image Data	GetImage.SlideSeq GetImage.STARmap GetImage.VisiumV1
Get integration data	GetIntegrationData
Calculate pearson residuals of features not in the scale.data	GetResidual
Get Tissue Coordinates	GetTissueCoordinates.SlideSeq GetTissueCoordinates.STARmap GetTissueCoordinates.VisiumV1
Get the predicted identity	GetTransferPredictions
The Graph Class	Graph-class
Compute the correlation of features broken down by groups with another covariate	GroupCorrelation
Boxplot of correlation of a variable (e.g. number of UMIs) with expression data	GroupCorrelationPlot
Hover Locator	HoverLocator
Demultiplex samples based on data from cell 'hashing'	HTODemux
Hashtag oligo heatmap	HTOHeatmap
Get Variable Feature Information	HVFInfo.SCTAssay
Visualize features in dimensional reduction space interactively	IFeaturePlot
Spatial Cluster Plots	ImageDimPlot
Spatial Feature Plots	ImageFeaturePlot
Integrate data	IntegrateData
Integrate low dimensional embeddings	IntegrateEmbeddings IntegrateEmbeddings.IntegrationAnchorSet IntegrateEmbeddings.TransferAnchorSet
The IntegrationAnchorSet Class	IntegrationAnchorSet IntegrationAnchorSet-class
The IntegrationData Class	IntegrationData IntegrationData-class
Visualize clusters spatially and interactively	ISpatialDimPlot
Visualize features spatially and interactively	ISpatialFeaturePlot
Determine statistical significance of PCA scores.	JackStraw
The JackStrawData Class	JackStrawData-class
JackStraw Plot	JackStrawPlot
L2-Normalize CCA	L2CCA
L2-normalization	L2Dim
Label clusters on a ggplot2-based scatter plot	LabelClusters
Add text labels to a ggplot2 plot	Labeler LabelPoints
Visualize spatial and clustering (dimensional reduction) data in a linked, interactive framework	LinkedDimPlot LinkedFeaturePlot LinkedPlot LinkedPlots
Load a 10x Genomics Visium Spatial Experiment into a 'Seurat' object	Load10X_Spatial
Load the Annoy index file	LoadAnnoyIndex
Load Curio Seeker data	LoadCurioSeeker
Load STARmap data	LoadSTARmap
Read and Load 10x Genomics Xenium in-situ data	LoadXenium ReadXenium
Calculate the local structure preservation metric	LocalStruct
Normalize raw data	LogNormalize
Calculate the variance to mean ratio of logged values	LogVMR
Metric for evaluating mapping success	MappingScore MappingScore.AnchorSet MappingScore.default
Map query cells to a reference	MapQuery
Merge SCTAssay objects	merge.SCTAssay
Aggregate expression of multiple features into a single feature	MetaFeature
Apply a ceiling and floor to all values in a matrix	MinMax
Calculates a mixing metric	MixingMetric
Differential expression heatmap for mixscape	MixscapeHeatmap
Linear discriminant analysis on pooled CRISPR screen data.	MixscapeLDA
The ModalityWeights Class	ModalityWeights ModalityWeights-class
Demultiplex samples based on classification method from MULTI-seq (McGinnis et al., bioRxiv 2018)	MULTIseqDemux
The Neighbor Class	Neighbor-class
Highlight Neighbors in DimPlot	NNPlot
Normalize Data	NormalizeData NormalizeData.Assay NormalizeData.default NormalizeData.Seurat
Significant genes from a PCA	PCASigGenes
Calculate the percentage of a vector above some threshold	PercentAbove
Calculate the percentage of all counts that belong to a given set of features	PercentageFeatureSet
Plot clusters as a tree	PlotClusterTree
Function to plot perturbation score distributions.	PlotPerturbScore
Polygon DimPlot	PolyDimPlot
Polygon FeaturePlot	PolyFeaturePlot
Predict value from nearest neighbors	PredictAssay
Function to prepare data for Linear Discriminant Analysis.	PrepLDA
Prepare object to run differential expression on SCT assay with multiple models	PrepSCTFindMarkers
Prepare an object list normalized with sctransform for integration.	PrepSCTIntegration
Project Dimensional reduction onto full dataset	ProjectDim
Project query into UMAP coordinates of a reference	ProjectUMAP ProjectUMAP.default ProjectUMAP.DimReduc ProjectUMAP.Seurat
Get Spot Radius	Radius.SlideSeq Radius.STARmap Radius.VisiumV1
Load in data from 10X	Read10X
Read 10X hdf5 file	Read10X_h5
Load a 10X Genomics Visium Image	Read10X_Image
Read10x Probe Metadata	Read10X_probe_metadata
Read and Load Akoya CODEX data	LoadAkoya ReadAkoya
Load in data from remote or local mtx files	ReadMtx
Read and Load Nanostring SMI data	LoadNanostring ReadNanostring
Read output from Parse Biosciences	ReadParseBio
Load Slide-seq spatial data	ReadSlideSeq
Read output from STARsolo	ReadSTARsolo
Read Data From Vitessce	LoadHuBMAPCODEX ReadVitessce
Read and Load MERFISH Input from Vizgen	LoadVizgen ReadVizgen
Regroup idents based on meta.data info	RegroupIdents
Normalize raw data to fractions	RelativeCounts
Rename Cells in an Object	RenameCells.SCTAssay RenameCells.SlideSeq RenameCells.STARmap RenameCells.VisiumV1
Single cell ridge plot	RidgePlot
Perform Canonical Correlation Analysis	RunCCA RunCCA.default RunCCA.Seurat
Run Independent Component Analysis on gene expression	RunICA RunICA.Assay RunICA.default RunICA.Seurat
Run Linear Discriminant Analysis	RunLDA RunLDA.Assay RunLDA.default RunLDA.Seurat
Run the mark variogram computation on a given position matrix and expression matrix.	RunMarkVario
Run Mixscape	RunMixscape
Compute Moran's I value.	RunMoransI
Run Principal Component Analysis	RunPCA RunPCA.Assay RunPCA.default RunPCA.Seurat
Run Supervised Latent Semantic Indexing	RunSLSI RunSLSI.Assay RunSLSI.default RunSLSI.Seurat
Run Supervised Principal Component Analysis	RunSPCA RunSPCA.Assay RunSPCA.default RunSPCA.Seurat
Run t-distributed Stochastic Neighbor Embedding	RunTSNE RunTSNE.DimReduc RunTSNE.dist RunTSNE.matrix RunTSNE.Seurat
Run UMAP	RunUMAP RunUMAP.default RunUMAP.Graph RunUMAP.Neighbor RunUMAP.Seurat
Sample UMI	SampleUMI
Save the Annoy index	SaveAnnoyIndex
Scale and center the data.	ScaleData ScaleData.Assay ScaleData.default ScaleData.Seurat
Get image scale factors	ScaleFactors scalefactors ScaleFactors.VisiumV1
Compute Jackstraw scores significance.	ScoreJackStraw ScoreJackStraw.DimReduc ScoreJackStraw.JackStrawData ScoreJackStraw.Seurat
The SCTModel Class	levels.SCTAssay levels<-.SCTAssay SCTAssay SCTAssay-class SCTModel
Use regularized negative binomial regression to normalize UMI count data	SCTransform
Get SCT results from an Assay	SCTResults SCTResults.SCTAssay SCTResults.SCTModel SCTResults.Seurat SCTResults<- SCTResults<-.SCTAssay SCTResults<-.SCTModel
Select integration features	SelectIntegrationFeatures
Set integration data	SetIntegrationData
Find the Quantile of Data	SetQuantile
The Seurat Class	Seurat-class
The SeuratCommand Class	SeuratCommand-class
Seurat Themes	BoldTitle CenterTitle DarkTheme FontSize NoAxes NoGrid NoLegend RestoreLegend RotatedAxis SeuratAxes SeuratTheme SpatialTheme WhiteBackground
The SlideSeq class	SlideSeq SlideSeq-class
The SpatialImage Class	SpatialImage-class
Visualize spatial clustering and expression data.	SpatialDimPlot SpatialFeaturePlot SpatialPlot
Splits object into a list of subsetted objects.	SplitObject
The STARmap class	STARmap STARmap-class
Subset an AnchorSet object	subset.AnchorSet
Subset a Seurat Object based on the Barcode Distribution Inflection Points	SubsetByBarcodeInflections
Find cells with highest scores for a given dimensional reduction technique	TopCells
Find features with highest scores for a given dimensional reduction technique	TopFeatures
Get nearest neighbors for given cell	TopNeighbors
The TransferAnchorSet Class	TransferAnchorSet TransferAnchorSet-class
Transfer data	TransferData
Update pre-V4 Assays generated with SCTransform in the Seurat to the new SCTAssay class	UpdateSCTAssays
Get updated synonyms for gene symbols	GeneSymbolThesarus UpdateSymbolList
View variable features	MeanVarPlot VariableFeaturePlot VariableGenePlot
The VisiumV1 class	VisiumV1 VisiumV1-class
Visualize Dimensional Reduction genes	VizDimLoadings
Single cell violin plot	VlnPlot

Package: Seurat 4.4.0

Seurat: Tools for Single Cell Genomics

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