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Seurat v4.1

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

58,682

Version

4.1.0

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/satijalab/seurat

Homepage

https://satijalab.org/seurat

Maintainer

Paul Hoffman

Last Published

January 14th, 2022

Functions in Seurat (4.1.0)

Calculate module scores for feature expression programs in single cells

The Assay Class

AnchorSet-class

The AnchorSet Class

AddAzimuthResults

Add Azimuth Results

Automagically calculate a point size for ggplot2-based scatter plots

AverageExpression

Averaged feature expression by identity class

Augments ggplot2-based plot with a PNG image.

AnnotateAnchors

Add info to anchor matrix

AddAzimuthScores

Add Azimuth Scores

CalculateBarcodeInflections

Calculate the Barcode Distribution Inflection

CellCycleScoring

Score cell cycle phases

CreateSCTAssayObject

Create a SCT Assay object

Dimensional reduction plot

Combine ggplot2-based plots into a single plot

Dimensional reduction heatmap

AggregateExpression

Aggregated feature expression by identity class

Dot plot visualization

Feature expression heatmap

BuildClusterTree

Phylogenetic Analysis of Identity Classes

DE and EnrichR pathway visualization barplot

Match the case of character vectors

Scatter plot of single cell data

Calculate a perturbation Signature

BarcodeInflectionsPlot

Plot the Barcode Distribution and Calculated Inflection Points

Determine text color based on background color

CollapseSpeciesExpressionMatrix

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

FindMultiModalNeighbors

Construct weighted nearest neighbor graph

Gene expression markers of identity classes

Cell-cell scatter plot

Filter stray beads from Slide-seq puck

Run a custom distance function on an input data matrix

Create a custom color palette

Calculate the standard deviation of logged values

Calculate the variance of logged values

GetIntegrationData

Get integration data

Calculate pearson residuals of features not in the scale.data

CollapseEmbeddingOutliers

Move outliers towards center on dimension reduction plot

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

Color dimensional reduction plot by tree split

Gene expression markers for all identity classes

GroupCorrelationPlot

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

Cluster Determination

(Shared) Nearest-neighbor graph construction

Demultiplex samples based on data from cell 'hashing'

The DimReduc Class

FindSpatiallyVariableFeatures

Find spatially variable features

Quickly Pick Relevant Dimensions

FindConservedMarkers

Finds markers that are conserved between the groups

DiscretePalette

Discrete colour palettes from the pals package

FindVariableFeatures

Find variable features

Slim down a Seurat object

Visualize features in dimensional reduction space interactively

GetTissueCoordinates.SlideSeq

Get Tissue Coordinates

Calculate the mean of logged values

GetTransferPredictions

Get the predicted identity

Get an Assay object from a given Seurat object.

FindIntegrationAnchors

Find integration anchors

GetImage.SlideSeq

IntegrationAnchorSet-class

The IntegrationAnchorSet Class

L2-normalization

IntegrationData-class

The IntegrationData Class

The Graph Class

Label clusters on a ggplot2-based scatter plot

IntegrateEmbeddings

Integrate low dimensional embeddings

GroupCorrelation

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

Add text labels to a ggplot2 plot

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

Map query cells to a reference

L2-Normalize CCA

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

Normalize raw data

The Neighbor Class

Calculate the variance to mean ratio of logged values

PlotPerturbScore

Function to plot perturbation score distributions.

Visualize 'features' on a dimensional reduction plot

Scale and/or center matrix rowwise

Read 10X hdf5 file

Find subclusters under one cluster

Hashtag oligo heatmap

ISpatialFeaturePlot

Visualize features spatially and interactively

HVFInfo.SCTAssay

Get Variable Feature Information

ISpatialDimPlot

Visualize clusters spatially and interactively

MixscapeHeatmap

Differential expression heatmap for mixscape

Polygon DimPlot

Linear discriminant analysis on pooled CRISPR screen data.

Load STARmap data

Load Slide-seq spatial data

ModalityWeights-class

The ModalityWeights Class

Radius.SlideSeq

Get Spot Radius

Project query into UMAP coordinates of a reference

FindTransferAnchors

Find transfer anchors

Highlight Neighbors in DimPlot

Determine statistical significance of PCA scores.

PolyFeaturePlot

Polygon FeaturePlot

Calculate the local structure preservation metric

Load in data from remote or local mtx files

Normalize raw data to fractions

JackStrawData-class

The JackStrawData Class

Read output from Parse Biosciences

Load the Annoy index file

Load10X_Spatial

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

Apply a ceiling and floor to all values in a matrix

Read output from STARsolo

Compute Moran's I value.

Run Principal Component Analysis

RenameCells.SCTAssay

Rename Cells in an Object

Scale and center the data.

Get image scale factors

Calculates a mixing metric

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

Predict value from nearest neighbors

Plot a single expression by identity on a plot

Regroup idents based on meta.data info

A single heatmap from base R using image

contrast-theory

Get the intensity and/or luminance of a color

TransferAnchorSet-class

The TransferAnchorSet Class

VariableFeaturePlot

View variable features

The VisiumV1 class

Run Supervised Principal Component Analysis

Run Supervised Latent Semantic Indexing

Use regularized negative binomial regression to normalize UMI count data

Metric for evaluating mapping success

Function to prepare data for Linear Discriminant Analysis.

Merge SCTAssay objects

Calculate the percentage of a vector above some threshold

Load a 10X Genomics Visium Image

Significant genes from a PCA

Load in data from 10X

Run Independent Component Analysis on gene expression

Aggregate expression of multiple features into a single feature

The STARmap class

Single cell ridge plot

PrepSCTFindMarkers

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

SeuratCommand-class

The SeuratCommand Class

Get nearest neighbors for given cell

Find features with highest scores for a given dimensional reduction technique

Run Linear Discriminant Analysis

The SCTModel Class

PercentageFeatureSet

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

PlotClusterTree

Plot clusters as a tree

Run t-distributed Stochastic Neighbor Embedding

Perform Canonical Correlation Analysis

Compute Jackstraw scores significance.

PrepSCTIntegration

Prepare an object list normalized with sctransform for integration.

Project Dimensional reduction onto full dataset

Visualize spatial clustering and expression data.

Splits object into a list of subsetted objects.

SelectIntegrationFeatures

Select integration features

UpdateSymbolList

Get updated synonyms for gene symbols

UpdateSCTAssays

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

Cell cycle genes

Get SCT results from an Assay

cc.genes.updated.2019

Cell cycle genes: 2019 update

SingleRasterMap

A single heatmap from ggplot2 using geom_raster

Find the Quantile of Data

SetIntegrationData

Set integration data

The Seurat Class

SingleSpatialPlot

Base plotting function for all Spatial plots

Find cells with highest scores for a given dimensional reduction technique

SubsetByBarcodeInflections

Subset a Seurat Object based on the Barcode Distribution Inflection Points

Visualize Dimensional Reduction genes

Single cell violin plot

Save the Annoy index

A single correlation plot

Plot a single dimension

Seurat: Tools for Single Cell Genomics

The SlideSeq class

Convert objects to CellDataSet objects

as.Seurat.CellDataSet

Convert objects to Seurat objects

SpatialImage-class

The SpatialImage Class

Objects exported from other packages

subset.AnchorSet

Subset an AnchorSet object

as.SingleCellExperiment

Convert objects to SingleCellExperiment objects

as.sparse.H5Group