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Seurat v5

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

We are excited to release Seurat v5! This updates introduces new functionality for spatial, multimodal, and scalable single-cell analysis.

Seurat v5 is backwards-compatible with previous versions, so that users will continue to be able to re-run existing workflows.

Instructions, documentation, and tutorials can be found at:

https://satijalab.org/seurat

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

https://github.com/satijalab/seurat

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

39,699

Version

5.2.0

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/satijalab/seurat

Homepage

https://satijalab.org/seurat

Maintainer

Paul Hoffman

Last Published

January 13th, 2025

Functions in Seurat (5.2.0)

Seurat-CCA Integration

BuildClusterTree

Phylogenetic Analysis of Identity Classes

Determine text color based on background color

CalculateBarcodeInflections

Calculate the Barcode Distribution Inflection

BridgeReferenceSet-class

The BridgeReferenceSet Class The BridgeReferenceSet is an output from PrepareBridgeReference

BarcodeInflectionsPlot

Plot the Barcode Distribution and Calculated Inflection Points

BridgeCellsRepresentation

Construct a dictionary representation for each unimodal dataset

BuildNicheAssay

Construct an assay for spatial niche analysis

Calculate a perturbation Signature

Calculate dispersion of features

CollapseSpeciesExpressionMatrix

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

CollapseEmbeddingOutliers

Move outliers towards center on dimension reduction plot

Match the case of character vectors

Cell-cell scatter plot

Color dimensional reduction plot by tree split

CellCycleScoring

Score cell cycle phases

Combine ggplot2-based plots into a single plot

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

Find variable features based on dispersion

Dimensional reduction heatmap

Dimensional reduction plot

DE and EnrichR pathway visualization barplot

Create a custom color palette

Run a custom distance function on an input data matrix

CreateSCTAssayObject

Create a SCT Assay object

FastRPCAIntegration

Perform integration on the joint PCA cell embeddings.

Scale and/or center matrix rowwise

The DimReduc Class

DiscretePalette

Discrete colour palettes from pals

Feature expression heatmap

Dot plot visualization

Slim down a Seurat object

Calculate the standard deviation of logged values

Visualize 'features' on a dimensional reduction plot

Scatter plot of single cell data

Calculate the variance of logged values

FetchResiduals_reference

temporal function to get residuals from reference

Filter stray beads from Slide-seq puck

FindBridgeTransferAnchors

Find bridge anchors between query and extended bridge-reference

Calculate the mean of logged values

CreateCategoryMatrix

Create one hot matrix for a given label

Generate CountSketch random matrix

Quickly Pick Relevant Dimensions

FindBridgeIntegrationAnchors

Find integration bridge anchors between query and extended bridge-reference

FetchResidualSCTModel

Calculate pearson residuals of features not in the scale.data This function is the secondary function under FetchResiduals

Calculate pearson residuals of features not in the scale.data

Gene expression markers for all identity classes

FindBridgeAnchor

Find bridge anchors between two unimodal datasets

FindVariableFeatures

Find variable features

FindTransferAnchors

Find transfer anchors

FindConservedMarkers

Finds markers that are conserved between the groups

Cluster Determination

Calculate pearson residuals of features not in the scale.data

Find subclusters under one cluster

FindSpatiallyVariableFeatures

Find spatially variable features

GetIntegrationData

Get integration data

GetImage.SlideSeq

Get an Assay object from a given Seurat object.

GroupCorrelation

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

Hashtag oligo heatmap

GetTissueCoordinates.SlideSeq

Get Tissue Coordinates

The Graph Class

GetTransferPredictions

Get the predicted identity

HarmonyIntegration

Harmony Integration

(Shared) Nearest-neighbor graph construction

FindMultiModalNeighbors

Construct weighted nearest neighbor graph

GroupCorrelationPlot

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

Demultiplex samples based on data from cell 'hashing'

Visualize features in dimensional reduction space interactively

FindIntegrationAnchors

Find integration anchors

Gene expression markers of identity classes

ISpatialDimPlot

Visualize clusters spatially and interactively

Gaussian sketching

Determine statistical significance of PCA scores.

ISpatialFeaturePlot

Visualize features spatially and interactively

JackStrawData-class

The JackStrawData Class

Spatial Cluster Plots

IntegrationData-class

The IntegrationData Class

IntegrationAnchorSet-class

The IntegrationAnchorSet Class

Load10X_Spatial

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

Add text labels to a ggplot2 plot

HVFInfo.SCTAssay

Get Variable Feature Information

Label clusters on a ggplot2-based scatter plot

IntegrateLayers

Integrate Layers

IntegrateEmbeddings

Integrate low dimensional embeddings

L2-Normalize CCA

ImageFeaturePlot

Spatial Feature Plots

L2-normalization

Find variable features based on mean.var.plot

Aggregate expression of multiple features into a single feature

Load the Annoy index file

Metric for evaluating mapping success

LoadCurioSeeker

Load Curio Seeker data

Map query cells to a reference

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

Apply a ceiling and floor to all values in a matrix

JointPCAIntegration

Seurat-Joint PCA Integration

Load STARmap data

Calculates a mixing metric

Leverage Score Calculation

Calculate the variance to mean ratio of logged values

ModalityWeights-class

The ModalityWeights Class

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

Highlight Neighbors in DimPlot

PrepSCTFindMarkers

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

PrepSCTIntegration

Prepare an object list normalized with sctransform for integration.

Convert Neighbor class to an asymmetrical Graph class

PlotClusterTree

Plot clusters as a tree

Linear discriminant analysis on pooled CRISPR screen data.

PlotPerturbScore

Function to plot perturbation score distributions.

MixscapeHeatmap

Differential expression heatmap for mixscape

RPCAIntegration

Seurat-RPCA Integration

Significant genes from a PCA

Polygon DimPlot

PolyFeaturePlot

Polygon FeaturePlot

Project query into UMAP coordinates of a reference

Project full data to the sketch assay

Radius.SlideSeq

Get Spot Radius

Predict value from nearest neighbors

Calculate the local structure preservation metric

Calculate the percentage of a vector above some threshold

Normalize Raw Data

PercentageFeatureSet

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

Function to prepare data for Linear Discriminant Analysis.

Read and Load Nanostring SMI data

Read output from Parse Biosciences

The Neighbor Class

PrepareBridgeReference

Prepare the bridge and reference datasets

ProjectIntegration

Integrate embeddings from the integrated sketched.assay

ProjectDimReduc

Project query data to reference dimensional reduction

Read10X_ScaleFactors

Load 10X Genomics Visium Scale Factors

Load a 10X Genomics Visium Image

PseudobulkExpression

Pseudobulk Expression

Load in data from remote or local mtx files

Read and Load 10x Genomics Xenium in-situ data

Read and Load Akoya CODEX data

RunGraphLaplacian

Run Graph Laplacian Eigendecomposition

Read Data From Vitessce

Run Independent Component Analysis on gene expression

Read output from STARsolo

Project Dimensional reduction onto full dataset

Load Slide-seq spatial data

Regroup idents based on meta.data info

Read and Load MERFISH Input from Vizgen

ProjectCellEmbeddings

Project query data to the reference dimensional reduction

Read10X_Coordinates

Load 10X Genomics Visium Tissue Positions

Load in data from 10X

Run t-distributed Stochastic Neighbor Embedding

Normalize raw data to fractions

Run Supervised Principal Component Analysis

Run Supervised Latent Semantic Indexing

RenameCells.SCTAssay

Rename Cells in an Object

Run Leiden clustering algorithm

Run Linear Discriminant Analysis

Compute Moran's I value.

Run Principal Component Analysis

Read 10X hdf5 file

Single cell ridge plot

Perform Canonical Correlation Analysis

Read10X_probe_metadata

Read10x Probe Metadata

Save the Annoy index

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

The SCTModel Class

Get SCT results from an Assay

SelectIntegrationFeatures

Select integration features

Compute Jackstraw scores significance.

A single correlation plot

The Seurat Class

SelectSCTIntegrationFeatures

Select SCT integration features

SelectIntegrationFeatures5

Select integration features

Plot a single dimension

SeuratCommand-class

The SeuratCommand Class

The STARmap class

Perform sctransform-based normalization

Splits object into a list of subsetted objects.

Visualize spatial clustering and expression data.

SetIntegrationData

Set integration data

Find the Quantile of Data

SingleSpatialPlot

Base plotting function for all Spatial plots

Scale and center the data.

Get image scale factors

UpdateSCTAssays

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

SingleRasterMap

A single heatmap from ggplot2 using geom_raster

A single heatmap from base R using image

SingleImagePlot

Single Spatial Plot

UnSketchEmbeddings

Transfer embeddings from sketched cells to the full data

TransferSketchLabels

Transfer data from sketch data to full data

Plot a single expression by identity on a plot

Seurat: Tools for Single Cell Genomics

SubsetByBarcodeInflections

Subset a Seurat Object based on the Barcode Distribution Inflection Points

Find cells with highest scores for a given dimensional reduction technique

The SlideSeq class

UpdateSymbolList

Get updated synonyms for gene symbols

TransferAnchorSet-class

The TransferAnchorSet Class

SpatialImage-class

The SpatialImage Class

as.sparse.H5Group

as.SingleCellExperiment

Convert objects to SingleCellExperiment objects

The VisiumV1 class

The VisiumV2 class

contrast-theory

Get the intensity and/or luminance of a color

fortify-Spatial

Prepare Coordinates for Spatial Plots

Visualize Dimensional Reduction genes

Single cell violin plot

subset.AnchorSet

Subset an AnchorSet object

cc.genes.updated.2019

Cell cycle genes: 2019 update

Cell cycle genes

Variance Stabilizing Transformation

VariableFeaturePlot

View variable features

Find features with highest scores for a given dimensional reduction technique

Merge SCTAssay objects

writing-integration

Writing Integration Method Functions

Objects exported from other packages

Get nearest neighbors for given cell

Convert objects to CellDataSet objects

as.Seurat.CellDataSet

Convert objects to Seurat objects

Automagically calculate a point size for ggplot2-based scatter plots

AnnotateAnchors

Add info to anchor matrix

AddAzimuthScores

Add Azimuth Scores

Augments ggplot2-based plot with a PNG image.

Calculate module scores for feature expression programs in single cells

AverageExpression

Averaged feature expression by identity class

AddAzimuthResults

Add Azimuth Results

AnchorSet-class

The AnchorSet Class

AggregateExpression

Aggregated feature expression by identity class

The Assay Class