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Seurat v4.0

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:

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

48,395

Version

4.0.0

License

GPL-3 | file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/satijalab/seurat

Homepage

https://satijalab.org/seurat

Maintainer

Paul Hoffman

Last Published

January 30th, 2021

Functions in Seurat (4.0.0)

AggregateExpression

Aggregated feature expression by identity class

Augments ggplot2-based plot with a PNG image.

AnnotateAnchors

Add info to anchor matrix

AnchorSet-class

The AnchorSet Class

The Assay Class

BarcodeInflectionsPlot

Plot the Barcode Distribution and Calculated Inflection Points

Calculate module scores for feature expression programs in single cells

AverageExpression

Averaged feature expression by identity class

BuildClusterTree

Phylogenetic Analysis of Identity Classes

Match the case of character vectors

Create a custom color palette

Visualize 'features' on a dimensional reduction plot

FindSpatiallyVariableFeatures

Find spatially variable features

DE and EnrichR pathway visualization barplot

CreateSCTAssayObject

Create a SCT Assay object

Scatter plot of single cell data

Find subclusters under one cluster

Run a custom distance function on an input data matrix

Cell-cell scatter plot

FindTransferAnchors

Find transfer anchors

FindVariableFeatures

Find variable features

DiscretePalette

Discrete colour palettes from the pals package

Calculate a perturbation Signature

FindConservedMarkers

Finds markers that are conserved between the groups

Calculate the standard deviation of logged values

Calculate the mean of logged values

Cluster Determination

Get an Assay object from a given Seurat object.

CellCycleScoring

Score cell cycle phases

Hashtag oligo heatmap

Demultiplex samples based on data from cell 'hashing'

Determine statistical significance of PCA scores.

Slim down a Seurat object

GetTransferPredictions

Get the predicted identity

Dot plot visualization

Quickly Pick Relevant Dimensions

(Shared) Nearest-neighbor graph construction

CalculateBarcodeInflections

Calculate the Barcode Distribution Inflection

FindMultiModalNeighbors

Construct weighted nearest neighbor graph

Dimensional reduction heatmap

The Graph Class

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

JackStrawData-class

The JackStrawData Class

Feature expression heatmap

Filter stray beads from Slide-seq puck

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

Map query cells to a reference

CollapseEmbeddingOutliers

Move outliers towards center on dimension reduction plot

Determine text color based on background color

Combine ggplot2-based plots into a single plot

CollapseSpeciesExpressionMatrix

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

Color dimensional reduction plot by tree split

Dimensional reduction plot

Calculate the variance of logged values

The DimReduc Class

ModalityWeights-class

The ModalityWeights Class

Gene expression markers for all identity classes

Scale and/or center matrix rowwise

GetTissueCoordinates.SlideSeq

Get Tissue Coordinates

Highlight Neighbors in DimPlot

Calculate pearson residuals of features not in the scale.data

Project query into UMAP coordinates of a reference

Load STARmap data

IntegrateEmbeddings

Integrate low dimensional embeddings

GetImage.SlideSeq

L2-normalization

FindIntegrationAnchors

Find integration anchors

GetIntegrationData

Get integration data

Label clusters on a ggplot2-based scatter plot

GroupCorrelation

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

Load10X_Spatial

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

Calculate the local structure preservation metric

GroupCorrelationPlot

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

Gene expression markers of identity classes

MixscapeHeatmap

Differential expression heatmap for mixscape

Load the Annoy index file

L2-Normalize CCA

ISpatialDimPlot

Visualize clusters spatially and interactively

Linear discriminant analysis on pooled CRISPR screen data.

The Neighbor Class

PlotClusterTree

Plot clusters as a tree

RenameCells.SCTAssay

Rename Cells in an Object

PlotPerturbScore

Function to plot perturbation score distributions.

Normalize raw data

Calculate the variance to mean ratio of logged values

Predict value from nearest neighbors

Visualize features in dimensional reduction space interactively

Add text labels to a ggplot2 plot

ISpatialFeaturePlot

Visualize features spatially and interactively

Get image scale factors

Load in data from 10X

Load a 10X Genomics Visium Image

Scale and center the data.

Radius.SlideSeq

Get Spot Radius

PrepSCTIntegration

Prepare an object list normalized with sctransform for integration.

Project Dimensional reduction onto full dataset

Single cell ridge plot

The SCTModel Class

Seurat: Tools for Single Cell Genomics

SeuratCommand-class

The SeuratCommand Class

Find cells with highest scores for a given dimensional reduction technique

Get SCT results from an Assay

Save the Annoy index

IntegrationAnchorSet-class

The IntegrationAnchorSet Class

Convert objects to CellDataSet objects

Single cell violin plot

Find features with highest scores for a given dimensional reduction technique

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

Metric for evaluating mapping success

UpdateSCTAssays

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

Merge SCTAssay objects

Read 10X hdf5 file

subset.AnchorSet

Subset an AnchorSet object

IntegrationData-class

The IntegrationData Class

Run Principal Component Analysis

Load Slide-seq spatial data

PolyFeaturePlot

Polygon FeaturePlot

Apply a ceiling and floor to all values in a matrix

Calculates a mixing metric

Aggregate expression of multiple features into a single feature

Polygon DimPlot

Objects exported from other packages

Function to prepare data for Linear Discriminant Analysis.

Perform Canonical Correlation Analysis

Regroup idents based on meta.data info

Significant genes from a PCA

PercentageFeatureSet

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

Compute Jackstraw scores significance.

Normalize raw data to fractions

SpatialImage-class

The SpatialImage Class

Run t-distributed Stochastic Neighbor Embedding

SelectIntegrationFeatures

Select integration features

contrast-theory

Get the intensity and/or luminance of a color

Visualize spatial clustering and expression data.

cc.genes.updated.2019

Cell cycle genes: 2019 update

Run Independent Component Analysis on gene expression

Run Supervised Principal Component Analysis

UpdateSymbolList

Get updated synonyms for gene symbols

Compute Moran's I value.

VariableFeaturePlot

View variable features

as.Seurat.CellDataSet

Convert objects to Seurat objects

as.SingleCellExperiment

Convert objects to SingleCellExperiment objects

Run Linear Discriminant Analysis

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

SetIntegrationData

Set integration data

The Seurat Class

Use regularized negative binomial regression to normalize UMI count data

The STARmap class

Splits object into a list of subsetted objects.

SubsetByBarcodeInflections

Subset a Seurat Object based on the Barcode Distribution Inflection Points

as.sparse.H5Group

Cell cycle genes

The VisiumV1 class

Visualize Dimensional Reduction genes

Get nearest neighbors for given cell

The SlideSeq class

TransferAnchorSet-class

The TransferAnchorSet Class