Tools for Single Cell Genomics
Find features with highest scores for a given dimensional reduction te...
Get nearest neighbors for given cell
The TransferAnchorSet Class
Transfer data
The IntegrationData Class
Convert objects to Seurat objects
Convert objects to SingleCellExperiment objects
Scale and/or center matrix rowwise
Visualize clusters spatially and interactively
Add info to anchor matrix
Convert objects to CellDataSet objects
Add Azimuth Results
Add Azimuth Scores
Calculate module scores for feature expression programs in single cell...
Aggregated feature expression by identity class
The AnchorSet Class
Cast to Sparse
The Assay Class
Augments ggplot2-based plot with a PNG image.
Automagically calculate a point size for ggplot2-based scatter plots
Averaged feature expression by identity class
Plot the Barcode Distribution and Calculated Inflection Points
Determine text color based on background color
Visualize features spatially and interactively
Construct a dictionary representation for each unimodal dataset
The BridgeReferenceSet Class The BridgeReferenceSet is an output from ...
Phylogenetic Analysis of Identity Classes
Construct an assay for spatial niche analysis
Calculate dispersion of features
Calculate a perturbation Signature
Aggregate expression of multiple features into a single feature
Calculate the Barcode Distribution Inflection
Match the case of character vectors
Seurat-CCA Integration
Score cell cycle phases
Get Cell Names
Get a vector of cell names associated with an image (or set of images)
Cell-cell scatter plot
Cell Selector
Move outliers towards center on dimension reduction plot
Slim down a multi-species expression matrix, when only one species is ...
Color dimensional reduction plot by tree split
Combine ggplot2-based plots into a single plot
Get the intensity and/or luminance of a color
Generate CountSketch random matrix
Create one hot matrix for a given label
Apply a ceiling and floor to all values in a matrix
Create a SCT Assay object
Run a custom distance function on an input data matrix
Create a custom color palette
DE and EnrichR pathway visualization barplot
Slim down a Seurat object
Dimensional reduction heatmap
Dimensional reduction plot
The DimReduc Class
Discrete colour palettes from pals
Find variable features based on dispersion
Feature expression heatmap
Dot plot visualization
Quickly Pick Relevant Dimensions
Calculate the mean of logged values
Calculate the standard deviation of logged values
Calculate the variance of logged values
Perform integration on the joint PCA cell embeddings.
Visualize 'features' on a dimensional reduction plot
Scatter plot of single cell data
Calculate pearson residuals of features not in the scale.data
temporal function to get residuals from reference
Find bridge anchors between query and extended bridge-reference
Calculate pearson residuals of features not in the scale.data This fun...
Filter stray beads from Slide-seq puck
Gene expression markers for all identity classes
Find bridge anchors between two unimodal datasets
Find integration bridge anchors between query and extended bridge-refe...
Cluster Determination
Finds markers that are conserved between the groups
Find integration anchors
Gene expression markers of identity classes
Construct weighted nearest neighbor graph
(Shared) Nearest-neighbor graph construction
Find spatially variable features
Find subclusters under one cluster
Find transfer anchors
Find variable features
Fold Change
Prepare Coordinates for Spatial Plots
Gaussian sketching
Get an Assay object from a given Seurat object.
Get Image Data
Get integration data
Calculate pearson residuals of features not in the scale.data
Get Tissue Coordinates
Integrate Layers
Get the predicted identity
The Graph Class
Compute the correlation of features broken down by groups with another...
Boxplot of correlation of a variable (e.g. number of UMIs) with expres...
Harmony Integration
Hover Locator
Demultiplex samples based on data from cell 'hashing'
The IntegrationAnchorSet Class
Hashtag oligo heatmap
Get Variable Feature Information
Visualize features in dimensional reduction space interactively
Spatial Cluster Plots
Spatial Feature Plots
Integrate data
Integrate low dimensional embeddings
Determine statistical significance of PCA scores.
The JackStrawData Class
JackStraw Plot
Seurat-Joint PCA Integration
L2-Normalize CCA
L2-normalization
Label clusters on a ggplot2-based scatter plot
Add text labels to a ggplot2 plot
Leverage Score Calculation
Visualize spatial and clustering (dimensional reduction) data in a lin...
Load a 10x Genomics Visium Spatial Experiment into a Seurat object
Load the Annoy index file
Load Curio Seeker data
Load STARmap data
Calculate the local structure preservation metric
Normalize Raw Data
Calculate the variance to mean ratio of logged values
Metric for evaluating mapping success
Map query cells to a reference
Merge SCTAssay objects
Calculates a mixing metric
Differential expression heatmap for mixscape
Linear discriminant analysis on pooled CRISPR screen data.
The ModalityWeights Class
Demultiplex samples based on classification method from MULTI-seq (McG...
Find variable features based on mean.var.plot
The Neighbor Class
Plot clusters as a tree
Highlight Neighbors in DimPlot
Convert Neighbor class to an asymmetrical Graph class
Normalize Data
Significant genes from a PCA
Calculate the percentage of a vector above some threshold
Calculate the percentage of all counts that belong to a given set of f...
Function to plot perturbation score distributions.
Polygon DimPlot
Polygon FeaturePlot
Predict value from nearest neighbors
Prepare the bridge and reference datasets
A single heatmap from ggplot2 using geom_raster
Function to prepare data for Linear Discriminant Analysis.
Prepare object to run differential expression on SCT assay with multip...
Prepare an object list normalized with sctransform for integration.
Project query data to the reference dimensional reduction
Project full data to the sketch assay
Project Dimensional reduction onto full dataset
Project query data to reference dimensional reduction
Integrate embeddings from the integrated sketched.assay
Project query into UMAP coordinates of a reference
Pseudobulk Expression
Get Spot Radius
Subset a Seurat Object based on the Barcode Distribution Inflection Po...
Load in data from 10X
Load 10X Genomics Visium Tissue Positions
Read 10X hdf5 file
Load a 10X Genomics Visium Image
Read10x Probe Metadata
Load 10X Genomics Visium Scale Factors
Read and Load Akoya CODEX data
Read and Load 10x Genomics Xenium in-situ data
Load in data from remote or local mtx files
Read and Load Nanostring SMI data
Read output from Parse Biosciences
Load Slide-seq spatial data
Read output from STARsolo
Read Data From Vitessce
Read and Load MERFISH Input from Vizgen
The Seurat Class
Seurat: Tools for Single Cell Genomics
Objects exported from other packages
Regroup idents based on meta.data info
Normalize raw data to fractions
Rename Cells in an Object
Single cell ridge plot
Seurat-RPCA Integration
Perform Canonical Correlation Analysis
Run Graph Laplacian Eigendecomposition
Run Independent Component Analysis on gene expression
Run Linear Discriminant Analysis
Run the mark variogram computation on a given position matrix and expr...
The SeuratCommand Class
Find cells with highest scores for a given dimensional reduction techn...
Run Mixscape
Compute Moran's I value.
Run Principal Component Analysis
Run Supervised Latent Semantic Indexing
Run Supervised Principal Component Analysis
Run t-distributed Stochastic Neighbor Embedding
Run UMAP
Sample UMI
Save the Annoy index
Scale and center the data.
Get image scale factors
Compute Jackstraw scores significance.
The SCTModel Class
Perform sctransform-based normalization
Get SCT results from an Assay
Select integration features
Select integration features
Select SCT integration features
Set integration data
Find the Quantile of Data
Seurat Themes
A single correlation plot
Plot a single dimension
Plot a single expression by identity on a plot
A single heatmap from base R using image
Single Spatial Plot
Base plotting function for all Spatial plots
Sketch Data
The SlideSeq class
The SpatialImage Class
Visualize spatial clustering and expression data.
Splits object into a list of subsetted objects.
The STARmap class
Subset an AnchorSet object
Transfer data from sketch data to full data
Transfer embeddings from sketched cells to the full data
Update pre-V4 Assays generated with SCTransform in the Seurat to the n...
Get updated synonyms for gene symbols
View variable features
The VisiumV1 class
The VisiumV2 class
Visualize Dimensional Reduction genes
Single cell violin plot
Variance Stabilizing Transformation
Writing Integration Method Functions
A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Useful links