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