The Assay Class
Augments ggplot2-based plot with a PNG image.
ALRA Approximate Rank Selection Plot
Pull Assays or assay names
Calculate module scores for feature expression programs in single cells
Plot the Barcode Distribution and Calculated Inflection Points
Phylogenetic Analysis of Identity Classes
The AnchorSet Class
Add in metadata associated with either cells or features.
Averaged feature expression by identity class
CollapseSpeciesExpressionMatrix
Slim down a multi-species expression matrix, when only one species is primarily of interenst.
Cell selector
Get cells present in an object
Get cell names grouped by identity class
CollapseEmbeddingOutliers
Move outliers towards center on dimension reduction plot
CalculateBarcodeInflections
Calculate the Barcode Distribution Inflection
Color dimensional reduction plot by tree split
Match the case of character vectors
Combine ggplot2-based plots into a single plot
Get SeuratCommands
Create an Assay object
Run a custom distance function on an input data matrix
Create a DimReduc object
Create a custom color palette
Score cell cycle phases
Slim down a Seurat object
Get and set the default assay
Cell-cell scatter plot
Dimensional reduction heatmap
Create a Seurat object
Convert a peak matrix to a gene activity matrix
Dimensional reduction plot
Calculate the standard deviation of logged values
Calculate the variance of logged values
Feature expression heatmap
The Dimmensional Reduction Class
Visualize 'features' on a dimensional reduction plot
Dot plot visualization
Quickly Pick Relevant Dimensions
Export Seurat object for UCSC cell browser
The Graph Class
Get cell embeddings
Calculate the mean of logged values
Demultiplex samples based on data from cell 'hashing'
Scatter plot of single cell data
Gene expression markers for all identity classes
Find transfer anchors
Find variable features
Hashtag oligo heatmap
Cluster Determination
Is an object global/persistent?
Access cellular data
Finds markers that are conserved between the groups
Get, set, and manipulate an object's identity classes
Hover Locator
Label clusters on a ggplot2-based scatter plot
Determine statistical significance of PCA scores.
Get highly variable feature information
Get JackStraw information
Get an Assay object from a given Seurat object.
Find integration anchors
General accessor function for the Assay class
The JackStrawData Class
Add text labels to a ggplot2 plot
Run Independent Component Analysis on gene expression
Perform Canonical Correlation Analysis
Prepare an object list that has been run through SCTransform for integration
Polygon DimPlot
Plot clusters as a tree
Polygon FeaturePlot
SelectIntegrationFeatures
Select integration features
L2-Normalize CCA
L2-normalization
Integrate data
Calculate pearson residuals of features not in the scale.data
Get integation data
JackStraw Plot
SNN Graph Construction
Gene expression markers of identity classes
The IntegrationData Class
Setter for multimodal data
Tools for single-cell genomics
The SeuratCommand Class
Find cells with highest scores for a given dimensional reduction technique
Find features with highest scores for a given dimensional reduction technique
Convert objects to Seurat objects
Convert objects to SingleCellExperiment objects
Significant genes from a PCA
Calculate the local structure preservation metric
Identify cells matching certain criteria
Normalize Data
Get feature loadings
Read 10X hdf5 file
Load in data from 10X
Calculate the percentage of all counts that belong to a given set of features
Get and set project information
Get a key
Log a command
Calculates a mixing metric
Access miscellaneous data
Normalize raw data
Project Dimensional reduction onto full dataset
Single cell ridge plot
Rename cells
Calculate the variance to mean ratio of logged values
Pull DimReducs or DimReduc names
Demultiplex samples based on classification method from MULTI-seq (McGinnis et al., bioRxiv 2018)
Run Latent Semantic Indexing on binary count matrix
Run Principal Component Analysis
Aggregate expression of multiple features into a single feature
Normalize raw data to fractions
Rename assays in a Seurat
object
Regroup idents based on meta.data info
Term frequency-inverse document frequency
Scale and center the data.
Compute Jackstraw scores significance.
Use regularized negative binomial regression to normalize UMI count data
Apply a ceiling and floor to all values in a matrix
Sample UMI
Load in data from Alevin pipeline
Load in data from Alevin pipeline
Run Adaptively-thresholded Low Rank Approximation (ALRA)
Merge two matrices by rowname
Run UMAP
Run t-distributed Stochastic Neighbor Embedding
The Seurat Class
Return a subset of the Seurat object
Set integation data
SubsetByBarcodeInflections
Subset a Seurat Object based on the Barcode Distribution Inflection Points
Get and set variable feature information
Subset a Seurat object
Convert objects to CellDataSet objects
Visualize Dimensional Reduction genes
Convert a matrix (or Matrix) to the Graph class.
Get and set additional tool data
Get the standard deviations for an object
Update old Seurat object to accomodate new features
Transfer Labels
Coerce a SeuratCommand to a list
Get updated synonyms for gene symbols
Stop Cellbrowser web server
Seurat Themes
Single cell violin plot
Splits object into a list of subsetted objects.
Identify cells matching certain criteria
Convert between data frames and sparse matrices
Cell cycle genes
Merge Seurat Objects
Convert objects to loom objects
A small example version of the PBMC dataset
Cell cycle genes: 2019 update
View variable features
Read from and write to h5ad files
The Seurat Class
Print the results of a dimensional reduction analysis