Seurat

Calculate module scores for feature expression programs in single cells

Aggregated feature expression by identity class

The AnchorSet Class

Add info to anchor matrix

The Assay Class

Augments ggplot2-based plot with a PNG image.

Averaged feature expression by identity class

Determine text color based on background color

Plot the Barcode Distribution and Calculated Inflection Points

Phylogenetic Analysis of Identity Classes

Calculate a perturbation Signature

Calculate the Barcode Distribution Inflection

Match the case of character vectors

Score cell cycle phases

Cell-cell scatter plot

Cell Selector

Get Cell Names

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

Move outliers towards center on dimension reduction plot

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

Color dimensional reduction plot by tree split

Combine ggplot2-based plots into a single plot

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 the pals package

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

Scale and/or center matrix rowwise

Visualize 'features' on a dimensional reduction plot

Scatter plot of single cell data

Filter stray beads from Slide-seq puck

Gene expression markers for all identity classes

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

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

Get the predicted identity

The Graph Class

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

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

Demultiplex samples based on data from cell 'hashing'

Hashtag oligo heatmap

Get Variable Feature Information

Hover Locator

Visualize features in dimensional reduction space interactively

Visualize clusters spatially and interactively

Visualize features spatially and interactively

Integrate data

Integrate low dimensional embeddings

The IntegrationAnchorSet Class

The IntegrationData Class

Determine statistical significance of PCA scores.

The JackStrawData Class

JackStraw Plot

L2-Normalize CCA

L2-normalization

Label clusters on a ggplot2-based scatter plot

Add text labels to a ggplot2 plot

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

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

Load the Annoy index file

Load STARmap data

Calculate the local structure preservation metric

Normalize raw data

Calculate the variance to mean ratio of logged values

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

Map query cells to a reference

Metric for evaluating mapping success

Aggregate expression of multiple features into a single feature

Apply a ceiling and floor to all values in a matrix

Calculates a mixing metric

Differential expression heatmap for mixscape

Linear discriminant analysis on pooled CRISPR screen data.

The ModalityWeights Class

Highlight Neighbors in DimPlot

The Neighbor Class

Normalize Data

Significant genes from a PCA

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

Plot clusters as a tree

Function to plot perturbation score distributions.

Polygon DimPlot

Polygon FeaturePlot

Predict value from nearest neighbors

Function to prepare data for Linear Discriminant Analysis.

Prepare an object list normalized with sctransform for integration.

Project Dimensional reduction onto full dataset

Project query into UMAP coordinates of a reference

Get Spot Radius

Load in data from 10X

Load a 10X Genomics Visium Image

Read 10X hdf5 file

Load in data from remote or local mtx files

Load Slide-seq spatial data

Regroup idents based on meta.data info

Normalize raw data to fractions

Rename Cells in an Object

Single cell ridge plot

Perform Canonical Correlation Analysis

Run Independent Component Analysis on gene expression

Run Linear Discriminant Analysis

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

Run Mixscape

Compute Moran's I value.

Run Principal Component Analysis

Run Supervised Principal Component Analysis

Run t-distributed Stochastic Neighbor Embedding

Run UMAP

The SCTModel Class

Get SCT results from an Assay

Use regularized negative binomial regression to normalize UMI count data

The STARmap class

Sample UMI

Save the Annoy index

Scale and center the data.

Get image scale factors

Compute Jackstraw scores significance.

Select integration features

Set integration data

The Seurat Class

Seurat: Tools for Single Cell Genomics

The SeuratCommand Class

Seurat Themes

The SlideSeq class

The SpatialImage Class

Visualize spatial clustering and expression data.

Splits object into a list of subsetted objects.

Subset a Seurat Object based on the Barcode Distribution Inflection Points

Find cells with highest scores for a given dimensional reduction technique

Find features with highest scores for a given dimensional reduction technique

Get nearest neighbors for given cell

The TransferAnchorSet Class

Transfer data

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

Get updated synonyms for gene symbols

View variable features

The VisiumV1 class

Visualize Dimensional Reduction genes

Single cell violin plot

Convert objects to CellDataSet objects

Convert objects to Seurat objects

Convert objects to SingleCellExperiment objects

Cast to Sparse

Cell cycle genes

Cell cycle genes: 2019 update

Get the intensity and/or luminance of a color

Merge SCTAssay objects

Objects exported from other packages

Subset an AnchorSet object