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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

44,926

Version

5.0.1

License

MIT + file LICENSE

Issues

Pull Requests

Stars

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Repository

https://github.com/satijalab/seurat

Homepage

https://satijalab.org/seurat

Maintainer

Last Published

November 17th, 2023

Functions in Seurat (5.0.1)

Match the case of character vectors

CellCycleScoring

Score cell cycle phases

BridgeReferenceSet-class

The BridgeReferenceSet Class The BridgeReferenceSet is an output from PrepareBridgeReference

Run a custom distance function on an input data matrix

Cell-cell scatter plot

CreateSCTAssayObject

Create a SCT Assay object

Dimensional reduction plot

Dimensional reduction heatmap

Generate CountSketch random matrix

CollapseSpeciesExpressionMatrix

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

BarcodeInflectionsPlot

Plot the Barcode Distribution and Calculated Inflection Points

CollapseEmbeddingOutliers

Move outliers towards center on dimension reduction plot

CreateCategoryMatrix

Create one hot matrix for a given label

Slim down a Seurat object

DiscretePalette

Discrete colour palettes from pals

Find variable features based on dispersion

The DimReduc Class

Quickly Pick Relevant Dimensions

Calculate the mean of logged values

FastRPCAIntegration

Perform integration on the joint PCA cell embeddings.

Calculate the standard deviation of logged values

DE and EnrichR pathway visualization barplot

Color dimensional reduction plot by tree split

Combine ggplot2-based plots into a single plot

Create a custom color palette

Calculate pearson residuals of features not in the scale.data

FetchResidualSCTModel

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

Scale and/or center matrix rowwise

FetchResiduals_reference

temporal function to get residuals from reference

Filter stray beads from Slide-seq puck

Calculate dispersion of features

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

Visualize 'features' on a dimensional reduction plot

Calculate the variance of logged values

Scatter plot of single cell data

Gene expression markers for all identity classes

FindBridgeAnchor

Find bridge anchors between two unimodal datasets

Dot plot visualization

Feature expression heatmap

FindBridgeIntegrationAnchors

Find integration bridge anchors between query and extended bridge-reference

FindBridgeTransferAnchors

Find bridge anchors between query and extended bridge-reference

FindVariableFeatures

Find variable features

FindTransferAnchors

Find transfer anchors

FindIntegrationAnchors

Find integration anchors

GroupCorrelation

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

Gene expression markers of identity classes

The Graph Class

Find subclusters under one cluster

FindSpatiallyVariableFeatures

Find spatially variable features

GetTissueCoordinates.SlideSeq

Get Tissue Coordinates

GetTransferPredictions

Get the predicted identity

GroupCorrelationPlot

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

GetImage.SlideSeq

Get an Assay object from a given Seurat object.

HarmonyIntegration

Harmony Integration

FindMultiModalNeighbors

Construct weighted nearest neighbor graph

HVFInfo.SCTAssay

Get Variable Feature Information

(Shared) Nearest-neighbor graph construction

Cluster Determination

Gaussian sketching

IntegrationAnchorSet-class

The IntegrationAnchorSet Class

IntegrationData-class

The IntegrationData Class

Hashtag oligo heatmap

Calculate pearson residuals of features not in the scale.data

GetIntegrationData

Get integration data

Demultiplex samples based on data from cell 'hashing'

IntegrateEmbeddings

Integrate low dimensional embeddings

Visualize features in dimensional reduction space interactively

FindConservedMarkers

Finds markers that are conserved between the groups

ISpatialDimPlot

Visualize clusters spatially and interactively

Determine statistical significance of PCA scores.

JackStrawData-class

The JackStrawData Class

Calculate the variance to mean ratio of logged values

Apply a ceiling and floor to all values in a matrix

JointPCAIntegration

Seurat-Joint PCA Integration

L2-Normalize CCA

L2-normalization

Leverage Score Calculation

LoadCurioSeeker

Load Curio Seeker data

ImageFeaturePlot

Spatial Feature Plots

IntegrateLayers

Integrate Layers

Load STARmap data

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

Convert Neighbor class to an asymmetrical Graph class

ModalityWeights-class

The ModalityWeights Class

Highlight Neighbors in DimPlot

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

ISpatialFeaturePlot

Visualize features spatially and interactively

Spatial Cluster Plots

Calculate the local structure preservation metric

Normalize Raw Data

MixscapeHeatmap

Differential expression heatmap for mixscape

The Neighbor Class

PlotClusterTree

Plot clusters as a tree

Linear discriminant analysis on pooled CRISPR screen data.

PlotPerturbScore

Function to plot perturbation score distributions.

Polygon DimPlot

PolyFeaturePlot

Polygon FeaturePlot

Load the Annoy index file

Metric for evaluating mapping success

Load10X_Spatial

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

Aggregate expression of multiple features into a single feature

Project full data to the sketch assay

Project Dimensional reduction onto full dataset

Project query into UMAP coordinates of a reference

Map query cells to a reference

PercentageFeatureSet

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

Find variable features based on mean.var.plot

Label clusters on a ggplot2-based scatter plot

Add text labels to a ggplot2 plot

Calculate the percentage of a vector above some threshold

Read and Load Nanostring SMI data

Radius.SlideSeq

Get Spot Radius

RPCAIntegration

Seurat-RPCA Integration

PseudobulkExpression

Pseudobulk Expression

Read output from STARsolo

Load Slide-seq spatial data

Calculates a mixing metric

Significant genes from a PCA

Predict value from nearest neighbors

Function to prepare data for Linear Discriminant Analysis.

PrepSCTFindMarkers

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

RunGraphLaplacian

Run Graph Laplacian Eigendecomposition

Normalize raw data to fractions

RenameCells.SCTAssay

Rename Cells in an Object

Read output from Parse Biosciences

Read10X_probe_metadata

Read10x Probe Metadata

ProjectCellEmbeddings

Project query data to the reference dimensional reduction

Single cell ridge plot

Read 10X hdf5 file

PrepSCTIntegration

Prepare an object list normalized with sctransform for integration.

PrepareBridgeReference

Prepare the bridge and reference datasets

ProjectIntegration

Integrate embeddings from the integrated sketched.assay

ProjectDimReduc

Project query data to reference dimensional reduction

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

Run Linear Discriminant Analysis

Read and Load MERFISH Input from Vizgen

Read Data From Vitessce

Load in data from 10X

Run Principal Component Analysis

Regroup idents based on meta.data info

Run Independent Component Analysis on gene expression

Get SCT results from an Assay

Perform sctransform-based normalization

Run t-distributed Stochastic Neighbor Embedding

Run Supervised Principal Component Analysis

Get image scale factors

Compute Jackstraw scores significance.

SelectIntegrationFeatures5

Select integration features

Read and Load Akoya CODEX data

Load in data from remote or local mtx files

SelectIntegrationFeatures

Select integration features

A single heatmap from base R using image

The STARmap class

Perform Canonical Correlation Analysis

Compute Moran's I value.

SingleImagePlot

Single Spatial Plot

Save the Annoy index

Run Supervised Latent Semantic Indexing

Find features with highest scores for a given dimensional reduction technique

Find cells with highest scores for a given dimensional reduction technique

Scale and center the data.

Find the Quantile of Data

Seurat: Tools for Single Cell Genomics

Load a 10X Genomics Visium Image

SingleRasterMap

A single heatmap from ggplot2 using geom_raster

Read and Load 10x Genomics Xenium in-situ data

The Seurat Class

The SCTModel Class

SpatialImage-class

The SpatialImage Class

Visualize spatial clustering and expression data.

UpdateSymbolList

Get updated synonyms for gene symbols

Visualize Dimensional Reduction genes

Variance Stabilizing Transformation

Single cell violin plot

SeuratCommand-class

The SeuratCommand Class

SetIntegrationData

Set integration data

SelectSCTIntegrationFeatures

Select SCT integration features

Plot a single dimension

as.SingleCellExperiment

Convert objects to SingleCellExperiment objects

TransferSketchLabels

Transfer data from sketch data to full data

as.sparse.H5Group

Get nearest neighbors for given cell

Merge SCTAssay objects

TransferAnchorSet-class

The TransferAnchorSet Class

Objects exported from other packages

A single correlation plot

UnSketchEmbeddings

Transfer embeddings from sketched cells to the full data

as.Seurat.CellDataSet

Convert objects to Seurat objects

SubsetByBarcodeInflections

Subset a Seurat Object based on the Barcode Distribution Inflection Points

UpdateSCTAssays

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

SingleSpatialPlot

Base plotting function for all Spatial plots

Splits object into a list of subsetted objects.

contrast-theory

Get the intensity and/or luminance of a color

Convert objects to CellDataSet objects

VariableFeaturePlot

View variable features

Plot a single expression by identity on a plot

The VisiumV1 class

subset.AnchorSet

Subset an AnchorSet object

The SlideSeq class

fortify-Spatial

Prepare Coordinates for Spatial Plots

Cell cycle genes

cc.genes.updated.2019

Cell cycle genes: 2019 update

writing-integration

Writing Integration Method Functions

AnchorSet-class

The AnchorSet Class

AddAzimuthScores

Add Azimuth Scores

AverageExpression

Averaged feature expression by identity class

AddAzimuthResults

Add Azimuth Results

Automagically calculate a point size for ggplot2-based scatter plots

AnnotateAnchors

Add info to anchor matrix

Calculate module scores for feature expression programs in single cells

Augments ggplot2-based plot with a PNG image.

AggregateExpression

Aggregated feature expression by identity class

The Assay Class

Calculate a perturbation Signature

Determine text color based on background color

BuildNicheAssay

Construct an assay for spatial niche analysis

BuildClusterTree

Phylogenetic Analysis of Identity Classes

Seurat-CCA Integration

CalculateBarcodeInflections

Calculate the Barcode Distribution Inflection

BridgeCellsRepresentation

Construct a dictionary representation for each unimodal dataset