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Seurat v4.3.0

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

58,682

Version

4.3.0

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

November 18th, 2022

Functions in Seurat (4.3.0)

CellCycleScoring

Score cell cycle phases

Cell-cell scatter plot

Run a custom distance function on an input data matrix

Create a custom color palette

Dimensional reduction heatmap

Dimensional reduction plot

AddAzimuthResults

Add Azimuth Results

AddAzimuthScores

Add Azimuth Scores

Gene expression markers for all identity classes

BuildClusterTree

Phylogenetic Analysis of Identity Classes

Cluster Determination

Get an Assay object from a given Seurat object.

Calculate a perturbation Signature

CollapseSpeciesExpressionMatrix

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

The Assay Class

GetImage.SlideSeq

Automagically calculate a point size for ggplot2-based scatter plots

Color dimensional reduction plot by tree split

AnchorSet-class

The AnchorSet Class

AverageExpression

Averaged feature expression by identity class

AnnotateAnchors

Add info to anchor matrix

Augments ggplot2-based plot with a PNG image.

Determine text color based on background color

GetTissueCoordinates.SlideSeq

Get Tissue Coordinates

Calculate module scores for feature expression programs in single cells

AggregateExpression

Aggregated feature expression by identity class

CalculateBarcodeInflections

Calculate the Barcode Distribution Inflection

Match the case of character vectors

BarcodeInflectionsPlot

Plot the Barcode Distribution and Calculated Inflection Points

Quickly Pick Relevant Dimensions

GetTransferPredictions

Get the predicted identity

Spatial Cluster Plots

Combine ggplot2-based plots into a single plot

DE and EnrichR pathway visualization barplot

Feature expression heatmap

Calculate the mean of logged values

ImageFeaturePlot

Spatial Feature Plots

Scale and/or center matrix rowwise

Visualize 'features' on a dimensional reduction plot

Dot plot visualization

IntegrateEmbeddings

Integrate low dimensional embeddings

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

CollapseEmbeddingOutliers

Move outliers towards center on dimension reduction plot

Load STARmap data

Calculate the local structure preservation metric

ModalityWeights-class

The ModalityWeights Class

L2-Normalize CCA

FindConservedMarkers

Finds markers that are conserved between the groups

FindIntegrationAnchors

Find integration anchors

Slim down a Seurat object

Highlight Neighbors in DimPlot

Project query into UMAP coordinates of a reference

Gene expression markers of identity classes

Radius.SlideSeq

Get Spot Radius

Normalize raw data

The DimReduc Class

CreateSCTAssayObject

Create a SCT Assay object

Find subclusters under one cluster

Calculate the standard deviation of logged values

Calculate the variance to mean ratio of logged values

Run Linear Discriminant Analysis

FindTransferAnchors

Find transfer anchors

PrepSCTIntegration

Prepare an object list normalized with sctransform for integration.

FindMultiModalNeighbors

Construct weighted nearest neighbor graph

Calculate the variance of logged values

GetIntegrationData

Get integration data

Hashtag oligo heatmap

Calculate pearson residuals of features not in the scale.data

DiscretePalette

Discrete colour palettes from pals

HVFInfo.SCTAssay

Get Variable Feature Information

Determine statistical significance of PCA scores.

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

Scatter plot of single cell data

Project Dimensional reduction onto full dataset

The Graph Class

JackStrawData-class

The JackStrawData Class

Read output from Parse Biosciences

Run Principal Component Analysis

Run Supervised Latent Semantic Indexing

GroupCorrelation

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

(Shared) Nearest-neighbor graph construction

Add text labels to a ggplot2 plot

Filter stray beads from Slide-seq puck

Apply a ceiling and floor to all values in a matrix

Read output from STARsolo

FindSpatiallyVariableFeatures

Find spatially variable features

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

The Neighbor Class

Calculates a mixing metric

Load in data from 10X

Load a 10X Genomics Visium Image

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

Plot a single dimension

Compute Moran's I value.

FindVariableFeatures

Find variable features

Plot a single expression by identity on a plot

GroupCorrelationPlot

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

Get SCT results from an Assay

Demultiplex samples based on data from cell 'hashing'

Visualize spatial clustering and expression data.

Load Slide-seq spatial data

Map query cells to a reference

Splits object into a list of subsetted objects.

Significant genes from a PCA

Calculate the percentage of a vector above some threshold

Read Data From Vitessce

Use regularized negative binomial regression to normalize UMI count data

as.SingleCellExperiment

Convert objects to SingleCellExperiment objects

Run Supervised Principal Component Analysis

Visualize features in dimensional reduction space interactively

ISpatialDimPlot

Visualize clusters spatially and interactively

as.sparse.H5Group

IntegrationAnchorSet-class

The IntegrationAnchorSet Class

ISpatialFeaturePlot

Visualize features spatially and interactively

Run t-distributed Stochastic Neighbor Embedding

L2-normalization

Label clusters on a ggplot2-based scatter plot

SelectIntegrationFeatures

Select integration features

SetIntegrationData

Set integration data

Read and Load MERFISH Input from Vizgen

Get image scale factors

MixscapeHeatmap

Differential expression heatmap for mixscape

Compute Jackstraw scores significance.

Linear discriminant analysis on pooled CRISPR screen data.

TransferAnchorSet-class

The TransferAnchorSet Class

Read and Load 10x Genomics Xenium in-situ data

IntegrationData-class

The IntegrationData Class

PercentageFeatureSet

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

Load10X_Spatial

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

Load the Annoy index file

Perform Canonical Correlation Analysis

Run Independent Component Analysis on gene expression

PlotClusterTree

Plot clusters as a tree

contrast-theory

Get the intensity and/or luminance of a color

fortify-Spatial

Prepare Coordinates for Spatial Plots

Metric for evaluating mapping success

PolyFeaturePlot

Polygon FeaturePlot

The SlideSeq class

Aggregate expression of multiple features into a single feature

PlotPerturbScore

Function to plot perturbation score distributions.

Polygon DimPlot

Function to prepare data for Linear Discriminant Analysis.

PrepSCTFindMarkers

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

Read 10X hdf5 file

Read and Load Akoya CODEX data

The SCTModel Class

Save the Annoy index

RenameCells.SCTAssay

Rename Cells in an Object

Scale and center the data.

Single cell ridge plot

SpatialImage-class

The SpatialImage Class

Find features with highest scores for a given dimensional reduction technique

The STARmap class

Find the Quantile of Data

Predict value from nearest neighbors

Get nearest neighbors for given cell

The VisiumV1 class

VariableFeaturePlot

View variable features

A single correlation plot

The Seurat Class

SubsetByBarcodeInflections

Subset a Seurat Object based on the Barcode Distribution Inflection Points

Load in data from remote or local mtx files

Read and Load Nanostring SMI data

subset.AnchorSet

Subset an AnchorSet object

Find cells with highest scores for a given dimensional reduction technique

Convert objects to CellDataSet objects

A single heatmap from base R using image

SingleImagePlot

Single Spatial Plot

as.Seurat.CellDataSet

Convert objects to Seurat objects

Cell cycle genes

cc.genes.updated.2019

Cell cycle genes: 2019 update

Merge SCTAssay objects

Regroup idents based on meta.data info

Objects exported from other packages

Normalize raw data to fractions

Seurat: Tools for Single Cell Genomics

SeuratCommand-class

The SeuratCommand Class

SingleRasterMap

A single heatmap from ggplot2 using geom_raster

SingleSpatialPlot

Base plotting function for all Spatial plots

UpdateSCTAssays

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

UpdateSymbolList

Get updated synonyms for gene symbols

Visualize Dimensional Reduction genes

Single cell violin plot