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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

54,321

Version

4.0.5

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

October 17th, 2021

Functions in Seurat (4.0.5)

AnnotateAnchors

Add info to anchor matrix

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

Determine text color based on background color

CalculateBarcodeInflections

Calculate the Barcode Distribution Inflection

Calculate a perturbation Signature

Augments ggplot2-based plot with a PNG image.

Run a custom distance function on an input data matrix

CreateSCTAssayObject

Create a SCT Assay object

Calculate the variance of logged values

Scale and/or center matrix rowwise

Dimensional reduction heatmap

BuildClusterTree

Phylogenetic Analysis of Identity Classes

BarcodeInflectionsPlot

Plot the Barcode Distribution and Calculated Inflection Points

Slim down a Seurat object

DiscretePalette

Discrete colour palettes from the pals package

The DimReduc Class

Dimensional reduction plot

AddAzimuthResults

Add Azimuth Results

Match the case of character vectors

AddAzimuthScores

Add Azimuth Scores

CellCycleScoring

Score cell cycle phases

AggregateExpression

Aggregated feature expression by identity class

Feature expression heatmap

CollapseEmbeddingOutliers

Move outliers towards center on dimension reduction plot

CollapseSpeciesExpressionMatrix

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

FindConservedMarkers

Finds markers that are conserved between the groups

Cluster Determination

DE and EnrichR pathway visualization barplot

Calculate the mean of logged values

Create a custom color palette

FindIntegrationAnchors

Find integration anchors

FindMultiModalNeighbors

Construct weighted nearest neighbor graph

Cell-cell scatter plot

FindSpatiallyVariableFeatures

Find spatially variable features

(Shared) Nearest-neighbor graph construction

Calculate the standard deviation of logged values

Find subclusters under one cluster

Filter stray beads from Slide-seq puck

Gene expression markers for all identity classes

FindTransferAnchors

Find transfer anchors

Get an Assay object from a given Seurat object.

HVFInfo.SCTAssay

Get Variable Feature Information

Gene expression markers of identity classes

IntegrationData-class

The IntegrationData Class

Color dimensional reduction plot by tree split

The Graph Class

GetTransferPredictions

Get the predicted identity

Visualize features in dimensional reduction space interactively

FindVariableFeatures

Find variable features

ISpatialDimPlot

Visualize clusters spatially and interactively

Quickly Pick Relevant Dimensions

Visualize 'features' on a dimensional reduction plot

GetImage.SlideSeq

Combine ggplot2-based plots into a single plot

Dot plot visualization

GetIntegrationData

Get integration data

Scatter plot of single cell data

L2-normalization

L2-Normalize CCA

IntegrateEmbeddings

Integrate low dimensional embeddings

Demultiplex samples based on data from cell 'hashing'

Hashtag oligo heatmap

Map query cells to a reference

Function to prepare data for Linear Discriminant Analysis.

IntegrationAnchorSet-class

The IntegrationAnchorSet Class

Metric for evaluating mapping success

GetTissueCoordinates.SlideSeq

Get Tissue Coordinates

GroupCorrelation

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

Calculate pearson residuals of features not in the scale.data

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

GroupCorrelationPlot

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

JackStrawData-class

The JackStrawData Class

Normalize raw data

Determine statistical significance of PCA scores.

Calculate the local structure preservation metric

Highlight Neighbors in DimPlot

The Neighbor Class

Calculates a mixing metric

Load10X_Spatial

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

Significant genes from a PCA

Load Slide-seq spatial data

Run Linear Discriminant Analysis

Read output from STARsolo

Label clusters on a ggplot2-based scatter plot

PrepSCTIntegration

Prepare an object list normalized with sctransform for integration.

Use regularized negative binomial regression to normalize UMI count data

The STARmap class

MixscapeHeatmap

Differential expression heatmap for mixscape

SetIntegrationData

Set integration data

The Seurat Class

ISpatialFeaturePlot

Visualize features spatially and interactively

Load the Annoy index file

Find cells with highest scores for a given dimensional reduction technique

Load STARmap data

Linear discriminant analysis on pooled CRISPR screen data.

Project Dimensional reduction onto full dataset

ModalityWeights-class

The ModalityWeights Class

Regroup idents based on meta.data info

Add text labels to a ggplot2 plot

Project query into UMAP coordinates of a reference

Normalize raw data to fractions

PlotPerturbScore

Function to plot perturbation score distributions.

Save the Annoy index

Load in data from remote or local mtx files

Perform Canonical Correlation Analysis

Polygon DimPlot

Read output from Parse Biosciences

Run Independent Component Analysis on gene expression

The SlideSeq class

UpdateSCTAssays

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

Find features with highest scores for a given dimensional reduction technique

subset.AnchorSet

Subset an AnchorSet object

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

Calculate the variance to mean ratio of logged values

UpdateSymbolList

Get updated synonyms for gene symbols

VariableFeaturePlot

View variable features

PercentageFeatureSet

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

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

Run Supervised Principal Component Analysis

Run Principal Component Analysis

PlotClusterTree

Plot clusters as a tree

Seurat: Tools for Single Cell Genomics

Run t-distributed Stochastic Neighbor Embedding

Aggregate expression of multiple features into a single feature

SeuratCommand-class

The SeuratCommand Class

Load a 10X Genomics Visium Image

Get nearest neighbors for given cell

Single cell ridge plot

Visualize spatial clustering and expression data.

SelectIntegrationFeatures

Select integration features

Read 10X hdf5 file

RenameCells.SCTAssay

Rename Cells in an Object

Visualize Dimensional Reduction genes

Compute Jackstraw scores significance.

The VisiumV1 class

SpatialImage-class

The SpatialImage Class

TransferAnchorSet-class

The TransferAnchorSet Class

Scale and center the data.

Single cell violin plot

Get image scale factors

Radius.SlideSeq

Get Spot Radius

Load in data from 10X

PolyFeaturePlot

Polygon FeaturePlot

Predict value from nearest neighbors

Apply a ceiling and floor to all values in a matrix

Compute Moran's I value.

The SCTModel Class

Cell cycle genes

as.sparse.H5Group

Merge SCTAssay objects

Objects exported from other packages

Get SCT results from an Assay

as.SingleCellExperiment

Convert objects to SingleCellExperiment objects

SubsetByBarcodeInflections

Subset a Seurat Object based on the Barcode Distribution Inflection Points

as.Seurat.CellDataSet

Convert objects to Seurat objects

Splits object into a list of subsetted objects.

cc.genes.updated.2019

Cell cycle genes: 2019 update

contrast-theory

Get the intensity and/or luminance of a color

Convert objects to CellDataSet objects

AverageExpression

Averaged feature expression by identity class

Calculate module scores for feature expression programs in single cells

The Assay Class

AnchorSet-class

The AnchorSet Class