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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

60,896

Version

4.0.3

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

June 10th, 2021

Functions in Seurat (4.0.3)

AnchorSet-class

The AnchorSet Class

Determine text color based on background color

CollapseEmbeddingOutliers

Move outliers towards center on dimension reduction plot

AverageExpression

Averaged feature expression by identity class

The DimReduc Class

AnnotateAnchors

Add info to anchor matrix

Calculate a perturbation Signature

Determine statistical significance of PCA scores.

AggregateExpression

Aggregated feature expression by identity class

Color dimensional reduction plot by tree split

subset.AnchorSet

Subset an AnchorSet object

The Assay Class

DiscretePalette

Discrete colour palettes from the pals package

CellCycleScoring

Score cell cycle phases

FindMultiModalNeighbors

Construct weighted nearest neighbor graph

BarcodeInflectionsPlot

Plot the Barcode Distribution and Calculated Inflection Points

AddAzimuthScores

Add Azimuth Scores

AddAzimuthResults

Add Azimuth Results

BuildClusterTree

Phylogenetic Analysis of Identity Classes

Combine ggplot2-based plots into a single plot

Dimensional reduction plot

Filter stray beads from Slide-seq puck

GetImage.SlideSeq

The Graph Class

Augments ggplot2-based plot with a PNG image.

JackStrawData-class

The JackStrawData Class

Visualize 'features' on a dimensional reduction plot

The STARmap class

CalculateBarcodeInflections

Calculate the Barcode Distribution Inflection

CollapseSpeciesExpressionMatrix

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

Get an Assay object from a given Seurat object.

Calculate module scores for feature expression programs in single cells

Gene expression markers for all identity classes

GetTransferPredictions

Get the predicted identity

GetIntegrationData

Get integration data

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

Map query cells to a reference

Find features with highest scores for a given dimensional reduction technique

Dimensional reduction heatmap

Slim down a Seurat object

Calculate the standard deviation of logged values

Calculate the mean of logged values

Calculate pearson residuals of features not in the scale.data

Quickly Pick Relevant Dimensions

Feature expression heatmap

Match the case of character vectors

FindConservedMarkers

Finds markers that are conserved between the groups

Cell-cell scatter plot

Scatter plot of single cell data

FindVariableFeatures

Find variable features

Calculate the variance of logged values

Create a custom color palette

DE and EnrichR pathway visualization barplot

ISpatialDimPlot

Visualize clusters spatially and interactively

CreateSCTAssayObject

Create a SCT Assay object

FindSpatiallyVariableFeatures

Find spatially variable features

ISpatialFeaturePlot

Visualize features spatially and interactively

Project Dimensional reduction onto full dataset

The Neighbor Class

Cluster Determination

Run a custom distance function on an input data matrix

Dot plot visualization

Highlight Neighbors in DimPlot

SetIntegrationData

Set integration data

GetTissueCoordinates.SlideSeq

Get Tissue Coordinates

The VisiumV1 class

Gene expression markers of identity classes

Significant genes from a PCA

Use regularized negative binomial regression to normalize UMI count data

Demultiplex samples based on data from cell 'hashing'

Load the Annoy index file

Calculate the local structure preservation metric

Scale and/or center matrix rowwise

IntegrationAnchorSet-class

The IntegrationAnchorSet Class

FindIntegrationAnchors

Find integration anchors

PrepSCTIntegration

Prepare an object list normalized with sctransform for integration.

IntegrateEmbeddings

Integrate low dimensional embeddings

Perform Canonical Correlation Analysis

Metric for evaluating mapping success

(Shared) Nearest-neighbor graph construction

Add text labels to a ggplot2 plot

Normalize raw data

HVFInfo.SCTAssay

Get Variable Feature Information

PlotClusterTree

Plot clusters as a tree

UpdateSCTAssays

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

Aggregate expression of multiple features into a single feature

IntegrationData-class

The IntegrationData Class

Regroup idents based on meta.data info

Visualize features in dimensional reduction space interactively

GroupCorrelation

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

Run Principal Component Analysis

TransferAnchorSet-class

The TransferAnchorSet Class

Find subclusters under one cluster

Cell cycle genes

Apply a ceiling and floor to all values in a matrix

Load STARmap data

FindTransferAnchors

Find transfer anchors

Load in data from 10X

Hashtag oligo heatmap

Get nearest neighbors for given cell

Get image scale factors

Calculate the variance to mean ratio of logged values

Scale and center the data.

Visualize spatial clustering and expression data.

PercentageFeatureSet

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

Function to prepare data for Linear Discriminant Analysis.

Run Supervised Principal Component Analysis

GroupCorrelationPlot

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

Run Linear Discriminant Analysis

Run Independent Component Analysis on gene expression

The Seurat Class

Read 10X hdf5 file

as.sparse.H5Group

PlotPerturbScore

Function to plot perturbation score distributions.

Polygon DimPlot

Run t-distributed Stochastic Neighbor Embedding

Load a 10X Genomics Visium Image

Normalize raw data to fractions

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

Find cells with highest scores for a given dimensional reduction technique

Compute Jackstraw scores significance.

L2-normalization

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

ModalityWeights-class

The ModalityWeights Class

Project query into UMAP coordinates of a reference

The SlideSeq class

as.SingleCellExperiment

Convert objects to SingleCellExperiment objects

Save the Annoy index

Label clusters on a ggplot2-based scatter plot

Visualize Dimensional Reduction genes

SelectIntegrationFeatures

Select integration features

as.Seurat.CellDataSet

Convert objects to Seurat objects

Radius.SlideSeq

Get Spot Radius

L2-Normalize CCA

Linear discriminant analysis on pooled CRISPR screen data.

Compute Moran's I value.

Single cell violin plot

Get SCT results from an Assay

Load in data from remote or local mtx files

Calculates a mixing metric

SubsetByBarcodeInflections

Subset a Seurat Object based on the Barcode Distribution Inflection Points

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

MixscapeHeatmap

Differential expression heatmap for mixscape

Splits object into a list of subsetted objects.

Single cell ridge plot

Load Slide-seq spatial data

RenameCells.SCTAssay

Rename Cells in an Object

cc.genes.updated.2019

Cell cycle genes: 2019 update

Load10X_Spatial

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

The SCTModel Class

SeuratCommand-class

The SeuratCommand Class

Seurat: Tools for Single Cell Genomics

contrast-theory

Get the intensity and/or luminance of a color

PolyFeaturePlot

Polygon FeaturePlot

Convert objects to CellDataSet objects

Objects exported from other packages

Predict value from nearest neighbors

SpatialImage-class

The SpatialImage Class

UpdateSymbolList

Get updated synonyms for gene symbols

Merge SCTAssay objects

VariableFeaturePlot

View variable features