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Seurat v4.2.1

Seurat is an R toolkit for single cell genomics, developed and maintained by the Satija Lab at NYGC.

Instructions, documentation, and tutorials can be found at:

Seurat is also hosted on GitHub, you can view and clone the repository at

Seurat has been successfully installed on Mac OS X, Linux, and Windows, using the devtools package to install directly from GitHub

Improvements and new features will be added on a regular basis, please post on the github page with any questions or if you would like to contribute

For a version history/changelog, please see the NEWS file.

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Version

Install

install.packages('Seurat')

Monthly Downloads

48,395

Version

4.2.1

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Maintainer

Paul Hoffman

Last Published

November 8th, 2022

Functions in Seurat (4.2.1)

AverageExpression

Averaged feature expression by identity class
AnchorSet-class

The AnchorSet Class
AddAzimuthResults

Add Azimuth Results
AutoPointSize

Automagically calculate a point size for ggplot2-based scatter plots
AnnotateAnchors

Add info to anchor matrix
AddModuleScore

Calculate module scores for feature expression programs in single cells
AggregateExpression

Aggregated feature expression by identity class
BarcodeInflectionsPlot

Plot the Barcode Distribution and Calculated Inflection Points
CaseMatch

Match the case of character vectors
Cells.SCTModel

Get Cell Names
BGTextColor

Determine text color based on background color
CellCycleScoring

Score cell cycle phases
CellSelector

Cell Selector
CalculateBarcodeInflections

Calculate the Barcode Distribution Inflection
CalcPerturbSig

Calculate a perturbation Signature
BuildClusterTree

Phylogenetic Analysis of Identity Classes
CellScatter

Cell-cell scatter plot
CollapseSpeciesExpressionMatrix

Slim down a multi-species expression matrix, when only one species is primarily of interenst.
CustomDistance

Run a custom distance function on an input data matrix
BlackAndWhite

Create a custom color palette
CollapseEmbeddingOutliers

Move outliers towards center on dimension reduction plot
CellsByImage

Get a vector of cell names associated with an image (or set of images)
DietSeurat

Slim down a Seurat object
DEenrichRPlot

DE and EnrichR pathway visualization barplot
ColorDimSplit

Color dimensional reduction plot by tree split
DimHeatmap

Dimensional reduction heatmap
ElbowPlot

Quickly Pick Relevant Dimensions
DotPlot

Dot plot visualization
DoHeatmap

Feature expression heatmap
ExpMean

Calculate the mean of logged values
DimPlot

Dimensional reduction plot
CombinePlots

Combine ggplot2-based plots into a single plot
CreateSCTAssayObject

Create a SCT Assay object
DimReduc-class

The DimReduc Class
DiscretePalette

Discrete colour palettes from the pals package
ExpVar

Calculate the variance of logged values
ExpSD

Calculate the standard deviation of logged values
FindAllMarkers

Gene expression markers for all identity classes
FeaturePlot

Visualize 'features' on a dimensional reduction plot
FindClusters

Cluster Determination
FindConservedMarkers

Finds markers that are conserved between the groups
FastRowScale

Scale and/or center matrix rowwise
FindIntegrationAnchors

Find integration anchors
FindMultiModalNeighbors

Construct weighted nearest neighbor graph
FindMarkers

Gene expression markers of identity classes
FeatureScatter

Scatter plot of single cell data
FilterSlideSeq

Filter stray beads from Slide-seq puck
GetResidual

Calculate pearson residuals of features not in the scale.data
FindVariableFeatures

Find variable features
FindNeighbors

(Shared) Nearest-neighbor graph construction
GetIntegrationData

Get integration data
GetAssay

Get an Assay object from a given Seurat object.
GetImage.SlideSeq

Get Image Data
FindSpatiallyVariableFeatures

Find spatially variable features
FindSubCluster

Find subclusters under one cluster
FoldChange

Fold Change
FindTransferAnchors

Find transfer anchors
HoverLocator

Hover Locator
Graph-class

The Graph Class
GetTissueCoordinates.SlideSeq

Get Tissue Coordinates
GroupCorrelation

Compute the correlation of features broken down by groups with another covariate
GetTransferPredictions

Get the predicted identity
HTODemux

Demultiplex samples based on data from cell 'hashing'
HTOHeatmap

Hashtag oligo heatmap
GroupCorrelationPlot

Boxplot of correlation of a variable (e.g. number of UMIs) with expression data
HVFInfo.SCTAssay

Get Variable Feature Information
IFeaturePlot

Visualize features in dimensional reduction space interactively
IntegrateData

Integrate data
IntegrationAnchorSet-class

The IntegrationAnchorSet Class
L2CCA

L2-Normalize CCA
JackStrawPlot

JackStraw Plot
IntegrationData-class

The IntegrationData Class
LocalStruct

Calculate the local structure preservation metric
LogVMR

Calculate the variance to mean ratio of logged values
LoadSTARmap

Load STARmap data
LogNormalize

Normalize raw data
IntegrateEmbeddings

Integrate low dimensional embeddings
LinkedPlots

Visualize spatial and clustering (dimensional reduction) data in a linked, interactive framework
LabelPoints

Add text labels to a ggplot2 plot
LoadAnnoyIndex

Load the Annoy index file
Load10X_Spatial

Load a 10x Genomics Visium Spatial Experiment into a Seurat object
MixscapeHeatmap

Differential expression heatmap for mixscape
MixscapeLDA

Linear discriminant analysis on pooled CRISPR screen data.
JackStraw

Determine statistical significance of PCA scores.
JackStrawData-class

The JackStrawData Class
NNPlot

Highlight Neighbors in DimPlot
ModalityWeights-class

The ModalityWeights Class
MULTIseqDemux

Demultiplex samples based on classification method from MULTI-seq (McGinnis et al., bioRxiv 2018)
MapQuery

Map query cells to a reference
L2Dim

L2-normalization
LabelClusters

Label clusters on a ggplot2-based scatter plot
MappingScore

Metric for evaluating mapping success
ISpatialDimPlot

Visualize clusters spatially and interactively
MetaFeature

Aggregate expression of multiple features into a single feature
ISpatialFeaturePlot

Visualize features spatially and interactively
PlotClusterTree

Plot clusters as a tree
PredictAssay

Predict value from nearest neighbors
PolyFeaturePlot

Polygon FeaturePlot
PercentageFeatureSet

Calculate the percentage of all counts that belong to a given set of features
MinMax

Apply a ceiling and floor to all values in a matrix
MixingMetric

Calculates a mixing metric
PercentAbove

Calculate the percentage of a vector above some threshold
PCASigGenes

Significant genes from a PCA
PlotPerturbScore

Function to plot perturbation score distributions.
NormalizeData

Normalize Data
Neighbor-class

The Neighbor Class
PolyDimPlot

Polygon DimPlot
PrepSCTIntegration

Prepare an object list normalized with sctransform for integration.
Read10X_h5

Read 10X hdf5 file
ProjectUMAP

Project query into UMAP coordinates of a reference
Radius.SlideSeq

Get Spot Radius
Read10X

Load in data from 10X
PrepLDA

Function to prepare data for Linear Discriminant Analysis.
PrepSCTFindMarkers

Prepare object to run differential expression on SCT assay with multiple models
ProjectDim

Project Dimensional reduction onto full dataset
ReadMtx

Load in data from remote or local mtx files
Read10X_Image

Load a 10X Genomics Visium Image
ReadParseBio

Read output from Parse Biosciences
ReadSTARsolo

Read output from STARsolo
RunCCA

Perform Canonical Correlation Analysis
RidgePlot

Single cell ridge plot
RunLDA

Run Linear Discriminant Analysis
RunICA

Run Independent Component Analysis on gene expression
ReadSlideSeq

Load Slide-seq spatial data
RegroupIdents

Regroup idents based on meta.data info
RenameCells.SCTAssay

Rename Cells in an Object
RelativeCounts

Normalize raw data to fractions
SCTAssay-class

The SCTModel Class
SCTResults

Get SCT results from an Assay
RunSPCA

Run Supervised Principal Component Analysis
RunSLSI

Run Supervised Latent Semantic Indexing
RunTSNE

Run t-distributed Stochastic Neighbor Embedding
RunUMAP

Run UMAP
RunMoransI

Compute Moran's I value.
ScoreJackStraw

Compute Jackstraw scores significance.
RunPCA

Run Principal Component Analysis
SelectIntegrationFeatures

Select integration features
ScaleFactors

Get image scale factors
SCTransform

Use regularized negative binomial regression to normalize UMI count data
ScaleData

Scale and center the data.
STARmap-class

The STARmap class
SetQuantile

Find the Quantile of Data
RunMarkVario

Run the mark variogram computation on a given position matrix and expression matrix.
RunMixscape

Run Mixscape
SetIntegrationData

Set integration data
SampleUMI

Sample UMI
SaveAnnoyIndex

Save the Annoy index
SeuratCommand-class

The SeuratCommand Class
SingleRasterMap

A single heatmap from ggplot2 using geom_raster
SingleCorPlot

A single correlation plot
SingleDimPlot

Plot a single dimension
Seurat-class

The Seurat Class
Seurat-package

Seurat: Tools for Single Cell Genomics
SeuratTheme

Seurat Themes
SingleSpatialPlot

Base plotting function for all Spatial plots
SubsetByBarcodeInflections

Subset a Seurat Object based on the Barcode Distribution Inflection Points
TopNeighbors

Get nearest neighbors for given cell
TopCells

Find cells with highest scores for a given dimensional reduction technique
SpatialImage-class

The SpatialImage Class
TopFeatures

Find features with highest scores for a given dimensional reduction technique
SplitObject

Splits object into a list of subsetted objects.
SlideSeq-class

The SlideSeq class
SpatialPlot

Visualize spatial clustering and expression data.
SingleExIPlot

Plot a single expression by identity on a plot
SingleImageMap

TransferData

Transfer data
TransferAnchorSet-class

The TransferAnchorSet Class
UpdateSymbolList

Get updated synonyms for gene symbols
as.Seurat.CellDataSet

Convert objects to Seurat objects
as.CellDataSet

Convert objects to CellDataSet objects
UpdateSCTAssays

Update pre-V4 Assays generated with SCTransform in the Seurat to the new SCTAssay class
as.SingleCellExperiment

Convert objects to SingleCellExperiment objects
VisiumV1-class

The VisiumV1 class
VariableFeaturePlot

View variable features
reexports

Objects exported from other packages
as.sparse.H5Group

Cast to Sparse
subset.AnchorSet

Subset an AnchorSet object
contrast-theory

Get the intensity and/or luminance of a color
merge.SCTAssay

Merge SCTAssay objects
VizDimLoadings

Visualize Dimensional Reduction genes
VlnPlot

Single cell violin plot
cc.genes.updated.2019

Cell cycle genes: 2019 update
cc.genes

Cell cycle genes
AddAzimuthScores

Add Azimuth Scores
Assay-class

The Assay Class
AugmentPlot

Augments ggplot2-based plot with a PNG image.