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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

49,115

Version

5.0.3

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/satijalab/seurat

Homepage

https://satijalab.org/seurat

Maintainer

Last Published

March 18th, 2024

Functions in Seurat (5.0.3)

AddAzimuthScores

Add Azimuth Scores

The Assay Class

Calculate module scores for feature expression programs in single cells

Augments ggplot2-based plot with a PNG image.

AnchorSet-class

The AnchorSet Class

AggregateExpression

Aggregated feature expression by identity class

BuildClusterTree

Phylogenetic Analysis of Identity Classes

BuildNicheAssay

Construct an assay for spatial niche analysis

Match the case of character vectors

CellCycleScoring

Score cell cycle phases

AnnotateAnchors

Add info to anchor matrix

Seurat-CCA Integration

Automagically calculate a point size for ggplot2-based scatter plots

AverageExpression

Averaged feature expression by identity class

BridgeCellsRepresentation

Construct a dictionary representation for each unimodal dataset

Dimensional reduction heatmap

Generate CountSketch random matrix

CreateCategoryMatrix

Create one hot matrix for a given label

Calculate dispersion of features

Dimensional reduction plot

Feature expression heatmap

Dot plot visualization

FetchResiduals_reference

temporal function to get residuals from reference

Cell-cell scatter plot

BridgeReferenceSet-class

The BridgeReferenceSet Class The BridgeReferenceSet is an output from PrepareBridgeReference

Filter stray beads from Slide-seq puck

Calculate a perturbation Signature

CalculateBarcodeInflections

Calculate the Barcode Distribution Inflection

FindBridgeIntegrationAnchors

Find integration bridge anchors between query and extended bridge-reference

CollapseEmbeddingOutliers

Move outliers towards center on dimension reduction plot

Color dimensional reduction plot by tree split

CreateSCTAssayObject

Create a SCT Assay object

Determine text color based on background color

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

FindBridgeTransferAnchors

Find bridge anchors between query and extended bridge-reference

Find variable features based on dispersion

FindTransferAnchors

Find transfer anchors

FindIntegrationAnchors

Find integration anchors

Combine ggplot2-based plots into a single plot

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

Gene expression markers of identity classes

Slim down a Seurat object

FastRPCAIntegration

Perform integration on the joint PCA cell embeddings.

GetIntegrationData

Get integration data

Create a custom color palette

FindVariableFeatures

Find variable features

The Graph Class

GroupCorrelation

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

Calculate pearson residuals of features not in the scale.data

Calculate the standard deviation of logged values

Run a custom distance function on an input data matrix

Scale and/or center matrix rowwise

The DimReduc Class

Calculate the variance of logged values

Gene expression markers for all identity classes

Hashtag oligo heatmap

IntegrateEmbeddings

Integrate low dimensional embeddings

Visualize 'features' on a dimensional reduction plot

DiscretePalette

Discrete colour palettes from pals

FindBridgeAnchor

Find bridge anchors between two unimodal datasets

IntegrateLayers

Integrate Layers

DE and EnrichR pathway visualization barplot

Quickly Pick Relevant Dimensions

FindMultiModalNeighbors

Construct weighted nearest neighbor graph

HVFInfo.SCTAssay

Get Variable Feature Information

Cluster Determination

Scatter plot of single cell data

FindConservedMarkers

Finds markers that are conserved between the groups

Polygon DimPlot

PolyFeaturePlot

Polygon FeaturePlot

Read Data From Vitessce

Significant genes from a PCA

IntegrationAnchorSet-class

The IntegrationAnchorSet Class

Map query cells to a reference

Find variable features based on mean.var.plot

ProjectDimReduc

Project query data to reference dimensional reduction

ProjectIntegration

Integrate embeddings from the integrated sketched.assay

Read and Load MERFISH Input from Vizgen

HarmonyIntegration

Harmony Integration

Run Principal Component Analysis

Calculate the mean of logged values

IntegrationData-class

The IntegrationData Class

Load10X_Spatial

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

Load the Annoy index file

(Shared) Nearest-neighbor graph construction

Determine statistical significance of PCA scores.

FetchResidualSCTModel

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

Function to prepare data for Linear Discriminant Analysis.

Highlight Neighbors in DimPlot

Normalize Raw Data

Run Supervised Latent Semantic Indexing

GetTransferPredictions

Get the predicted identity

GetTissueCoordinates.SlideSeq

Get Tissue Coordinates

ModalityWeights-class

The ModalityWeights Class

Predict value from nearest neighbors

Calculate the local structure preservation metric

Calculate pearson residuals of features not in the scale.data

Scale and center the data.

Save the Annoy index

Gaussian sketching

ISpatialFeaturePlot

Visualize features spatially and interactively

RunGraphLaplacian

Run Graph Laplacian Eigendecomposition

Read and Load Nanostring SMI data

Read output from Parse Biosciences

A single heatmap from base R using image

SingleImagePlot

Single Spatial Plot

SingleRasterMap

A single heatmap from ggplot2 using geom_raster

Spatial Cluster Plots

SingleSpatialPlot

Base plotting function for all Spatial plots

Add text labels to a ggplot2 plot

Label clusters on a ggplot2-based scatter plot

Aggregate expression of multiple features into a single feature

JackStrawData-class

The JackStrawData Class

Convert Neighbor class to an asymmetrical Graph class

Metric for evaluating mapping success

The Neighbor Class

UpdateSCTAssays

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

UnSketchEmbeddings

Transfer embeddings from sketched cells to the full data

FindSpatiallyVariableFeatures

Find spatially variable features

GroupCorrelationPlot

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

Run Independent Component Analysis on gene expression

Compute Moran's I value.

ImageFeaturePlot

Spatial Feature Plots

LoadCurioSeeker

Load Curio Seeker data

PlotClusterTree

Plot clusters as a tree

Find subclusters under one cluster

Get an Assay object from a given Seurat object.

Visualize features in dimensional reduction space interactively

ISpatialDimPlot

Visualize clusters spatially and interactively

JointPCAIntegration

Seurat-Joint PCA Integration

GetImage.SlideSeq

PlotPerturbScore

Function to plot perturbation score distributions.

Load STARmap data

SelectSCTIntegrationFeatures

Select SCT integration features

L2-Normalize CCA

SetIntegrationData

Set integration data

Seurat: Tools for Single Cell Genomics

PrepareBridgeReference

Prepare the bridge and reference datasets

Leverage Score Calculation

Calculate the variance to mean ratio of logged values

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

Load in data from 10X

Demultiplex samples based on data from cell 'hashing'

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

ProjectCellEmbeddings

Project query data to the reference dimensional reduction

Project query into UMAP coordinates of a reference

Load a 10X Genomics Visium Image

MixscapeHeatmap

Differential expression heatmap for mixscape

PrepSCTFindMarkers

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

Linear discriminant analysis on pooled CRISPR screen data.

Read 10X hdf5 file

L2-normalization

Apply a ceiling and floor to all values in a matrix

PrepSCTIntegration

Prepare an object list normalized with sctransform for integration.

Calculates a mixing metric

Read10X_probe_metadata

Read10x Probe Metadata

Run t-distributed Stochastic Neighbor Embedding

RenameCells.SCTAssay

Rename Cells in an Object

Normalize raw data to fractions

Plot a single expression by identity on a plot

Run Supervised Principal Component Analysis

Splits object into a list of subsetted objects.

Calculate the percentage of a vector above some threshold

Plot a single dimension

RPCAIntegration

Seurat-RPCA Integration

Radius.SlideSeq

Get Spot Radius

Run Linear Discriminant Analysis

PseudobulkExpression

Pseudobulk Expression

SubsetByBarcodeInflections

Subset a Seurat Object based on the Barcode Distribution Inflection Points

Read output from STARsolo

Load in data from remote or local mtx files

Project full data to the sketch assay

PercentageFeatureSet

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

Project Dimensional reduction onto full dataset

Read and Load Akoya CODEX data

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

SeuratCommand-class

The SeuratCommand Class

Get nearest neighbors for given cell

Load Slide-seq spatial data

SelectIntegrationFeatures

Select integration features

Read and Load 10x Genomics Xenium in-situ data

Regroup idents based on meta.data info

SpatialImage-class

The SpatialImage Class

TransferAnchorSet-class

The TransferAnchorSet Class

Visualize spatial clustering and expression data.

UpdateSymbolList

Get updated synonyms for gene symbols

SelectIntegrationFeatures5

Select integration features

The VisiumV1 class

A single correlation plot

VariableFeaturePlot

View variable features

Visualize Dimensional Reduction genes

Perform sctransform-based normalization

Single cell ridge plot

Perform Canonical Correlation Analysis

Get SCT results from an Assay

Cell cycle genes

Variance Stabilizing Transformation

as.SingleCellExperiment

Convert objects to SingleCellExperiment objects

Get image scale factors

Single cell violin plot

Compute Jackstraw scores significance.

Find cells with highest scores for a given dimensional reduction technique

Convert objects to CellDataSet objects

The Seurat Class

Find the Quantile of Data

Find features with highest scores for a given dimensional reduction technique

cc.genes.updated.2019

Cell cycle genes: 2019 update

as.sparse.H5Group

Merge SCTAssay objects

Objects exported from other packages

The SCTModel Class

as.Seurat.CellDataSet

Convert objects to Seurat objects

contrast-theory

Get the intensity and/or luminance of a color

The STARmap class

TransferSketchLabels

Transfer data from sketch data to full data

The SlideSeq class

fortify-Spatial

Prepare Coordinates for Spatial Plots

subset.AnchorSet

Subset an AnchorSet object

writing-integration

Writing Integration Method Functions

AddAzimuthResults

Add Azimuth Results