# Tools for Single Cell Genomics

## Documentation for package ‘Seurat’ version 3.0.0

- DESCRIPTION file.

## Help Pages

A B C D E F G H I J K L M N O P R S T U V W misc

## -- A --

AddMetaData | Add in metadata associated with either cells or features.
AddMetaData.Assay | Add in metadata associated with either cells or features.
AddMetaData.Seurat | Add in metadata associated with either cells or features.
AddModuleScore | Calculate module scores for feature expression programs in single cells
AddSamples | Merge Seurat Objects
ALRAChooseKPlot | ALRA Approximate Rank Selection Plot
AnchorSet | The AnchorSet Class
AnchorSet-class | The AnchorSet Class
as.data.frame.Matrix | Convert between data frames and sparse matrices
as.Graph | Convert a matrix (or Matrix) to the Graph class.
as.Graph.Matrix | Convert a matrix (or Matrix) to the Graph class.
as.Graph.matrix | Convert a matrix (or Matrix) to the Graph class.
as.loom | Convert objects to loom objects
as.loom.Seurat | Convert objects to loom objects
as.Seurat | Convert objects to Seurat objects
as.Seurat.loom | Convert objects to Seurat objects
as.Seurat.SingleCellExperiment | Convert objects to Seurat objects
as.SingleCellExperiment | Convert objects to SingleCellExperiment objects
as.SingleCellExperiment.Seurat | Convert objects to SingleCellExperiment objects
as.sparse | Convert between data frames and sparse matrices
as.sparse.data.frame | Convert between data frames and sparse matrices
as.sparse.H5Group | Convert between data frames and sparse matrices
as.sparse.Matrix | Convert between data frames and sparse matrices
as.sparse.matrix | Convert between data frames and sparse matrices
Assay | The Assay Class
Assay-class | The Assay Class
AugmentPlot | Augments ggplot2-based plot with a PNG image.
AverageExpression | Averaged feature expression by identity class

## -- B --

BarcodeInflectionsPlot | Plot the Barcode Distribution and Calculated Inflection Points
BlackAndWhite | Create a custom color palette
BlueAndRed | Create a custom color palette
BoldTitle | Seurat Themes
BuildClusterTree | Phylogenetic Analysis of Identity Classes

## -- C --

CalculateBarcodeInflections | Calculate the Barcode Distribution Inflection
CaseMatch | Match the case of character vectors
cc.genes | Cell cycle genes
CellCycleScoring | Score cell cycle phases
CellPlot | Cell-cell scatter plot
Cells | Get cells present in an object
Cells.default | Get cells present in an object
Cells.DimReduc | Get cells present in an object
CellScatter | Cell-cell scatter plot
CellSelector | Cell selector
CollapseSpeciesExpressionMatrix | Slim down a multi-species expression matrix, when only one species is primarily of interenst.
CombinePlots | Combine ggplot2-based plots into a single plot
Command | Get SeuratCommands
Command.Seurat | Get SeuratCommands
CreateAssayObject | Create an Assay object
CreateDimReducObject | Create a DimReduc object
CreateGeneActivityMatrix | Convert a peak matrix to a gene activity matrix
CreateSeuratObject | Create a Seurat object
CustomDistance | Run a custom distance function on an input data matrix
CustomPalette | Create a custom color palette

## -- D --

DarkTheme | Seurat Themes
DefaultAssay | Get and set the default assay
DefaultAssay.DimReduc | Get and set the default assay
DefaultAssay.Seurat | Get and set the default assay
DefaultAssay<- | Get and set the default assay
DefaultAssay<-.Seurat | Get and set the default assay
DietSeurat | Slim down a Seurat object
DimHeatmap | Dimensional reduction heatmap
DimPlot | Dimensional reduction plot
DimReduc | The Dimmensional Reduction Class
DimReduc-class | The Dimmensional Reduction Class
DoHeatmap | Feature expression heatmap
DotPlot | Dot plot visualization

## -- E --

ElbowPlot | Quickly Pick Relevant Dimensions
Embeddings | Get cell embeddings
Embeddings.DimReduc | Get cell embeddings
Embeddings.Seurat | Get cell embeddings
ExpMean | Calculate the mean of logged values
ExportToCellbrowser | Export Seurat object for UCSC cell browser
ExpSD | Calculate the standard deviation of logged values
ExpVar | Calculate the variance of logged values

## -- F --

FeatureHeatmap | Visualize 'features' on a dimensional reduction plot
FeatureLocator | Cell selector
FeaturePlot | Visualize 'features' on a dimensional reduction plot
FeatureScatter | Scatter plot of single cell data
FetchData | Access cellular data
FindAllMarkers | Gene expression markers for all identity classes
FindAllMarkersNode | Gene expression markers for all identity classes
FindClusters | Cluster Determination
FindClusters.default | Cluster Determination
FindClusters.Seurat | Cluster Determination
FindConservedMarkers | Finds markers that are conserved between the two groups
FindIntegrationAnchors | Find integration anchors
FindMarkers | Gene expression markers of identity classes
FindMarkers.default | Gene expression markers of identity classes
FindMarkers.Seurat | Gene expression markers of identity classes
FindMarkersNode | Gene expression markers of identity classes
FindNeighbors | SNN Graph Construction
FindNeighbors.Assay | SNN Graph Construction
FindNeighbors.default | SNN Graph Construction
FindNeighbors.dist | SNN Graph Construction
FindNeighbors.Seurat | SNN Graph Construction
FindTransferAnchors | Find transfer anchors
FindVariableFeatures | Find variable features
FindVariableFeatures.Assay | Find variable features
FindVariableFeatures.default | Find variable features
FindVariableFeatures.Seurat | Find variable features
FindVariableGenes | Find variable features
FontSize | Seurat Themes

## -- G --

GenePlot | Scatter plot of single cell data
GetAssay | Get an Assay object from a given Seurat object.
GetAssay.Seurat | Get an Assay object from a given Seurat object.
GetAssayData | General accessor function for the Assay class
GetAssayData.Assay | General accessor function for the Assay class
GetAssayData.Seurat | General accessor function for the Assay class
GetIntegrationData | Get integation data
Graph | The Graph Class
Graph-class | The Graph Class

## -- H --

HoverLocator | Hover Locator
HTODemux | Demultiplex samples based on data from cell 'hashing'
HTOHeatmap | Hashtag oligo heatmap
HVFInfo | Get highly variable feature information
HVFInfo.Assay | Get highly variable feature information
HVFInfo.Seurat | Get highly variable feature information

## -- I --

ICAPlot | Dimensional reduction plot
Idents | Get, set, and manipulate an object's identity classes
Idents.Seurat | Get, set, and manipulate an object's identity classes
Idents<- | Get, set, and manipulate an object's identity classes
Idents<-.Seurat | Get, set, and manipulate an object's identity classes
IntegrateData | Integrate data
IntegrationData | The IntegrationData Class
IntegrationData-class | The IntegrationData Class

## -- J --

JackStraw | Determine statistical significance of PCA scores.
JackStrawData | The JackStrawData Class
JackStrawData-class | The JackStrawData Class
JackStrawPlot | JackStraw Plot
JS | Get JackStraw information
JS.DimReduc | Get JackStraw information
JS.JackStrawData | Get JackStraw information
JS<- | Get JackStraw information
JS<-.DimReduc | Get JackStraw information
JS<-.JackStrawData | Get JackStraw information

## -- K --

Key | Get a key
Key.Assay | Get a key
Key.DimReduc | Get a key
Key.Seurat | Get a key
Key<- | Get a key
Key<-.Assay | Get a key
Key<-.DimReduc | Get a key

## -- L --

L2CCA | L2-Normalize CCA
L2Dim | L2-normalization
LabelClusters | Label clusters on a ggplot2-based scatter plot
Labeler | Add text labels to a ggplot2 plot
LabelPoints | Add text labels to a ggplot2 plot
levels.Seurat | Get, set, and manipulate an object's identity classes
levels<-.Seurat | Get, set, and manipulate an object's identity classes
Loadings | Get feature loadings
Loadings.DimReduc | Get feature loadings
Loadings.Seurat | Get feature loadings
Loadings<- | Get feature loadings
Loadings<-.DimReduc | Get feature loadings
LocalStruct | Calculate the local structure preservation metric
LogNormalize | Normalize raw data
LogVMR | Calculate the variance to mean ratio of logged values

## -- M --

MeanVarPlot | View variable features
merge | Merge Seurat Objects
merge.Assay | Merge Seurat Objects
merge.Seurat | Merge Seurat Objects
MergeSeurat | Merge Seurat Objects
MetaFeature | Aggregate expression of multiple features into a single feature
MinMax | Apply a ceiling and floor to all values in a matrix
Misc | Access miscellaneous data
Misc.Assay | Access miscellaneous data
Misc.Seurat | Access miscellaneous data
Misc<- | Access miscellaneous data
Misc<-.Assay | Access miscellaneous data
Misc<-.Seurat | Access miscellaneous data
MixingMetric | Calculates a mixing metric
MULTIseqDemux | Demultiplex samples based on classification method from MULTI-seq (McGinnis et al., bioRxiv 2018)

## -- N --

NoAxes | Seurat Themes
NoGrid | Seurat Themes
NoLegend | Seurat Themes
NormalizeData | Normalize Data
NormalizeData.Assay | Normalize Data
NormalizeData.default | Normalize Data
NormalizeData.Seurat | Normalize Data

## -- O --

OldWhichCells | Identify cells matching certain criteria
OldWhichCells.Assay | Identify cells matching certain criteria
OldWhichCells.Seurat | Identify cells matching certain criteria

## -- P --

pbmc_small | A small example version of the PBMC dataset
PCAPlot | Dimensional reduction plot
PCASigGenes | Significant genes from a PCA
PCHeatmap | Dimensional reduction heatmap
PercentageFeatureSet | Calculate the percentage of all counts that belong to a given set of features
PlotClusterTree | Plot clusters as a tree
PolyDimPlot | Polygon DimPlot
PolyFeaturePlot | Polygon FeaturePlot
print | Print the results of a dimensional reduction analysis
print.DimReduc | Print the results of a dimensional reduction analysis
Project | Get and set project information
Project.Seurat | Get and set project information
Project<- | Get and set project information
Project<-.Seurat | Get and set project information
ProjectDim | Project Dimensional reduction onto full dataset
PurpleAndYellow | Create a custom color palette

## -- R --

Read10X | Load in data from 10X
Read10X_h5 | Read 10X hdf5 file
ReadAlevin | Load in data from Alevin pipeline
ReadAlevinCsv | Load in data from Alevin pipeline
ReadH5AD | Read from and write to h5ad files
ReadH5AD.character | Read from and write to h5ad files
ReadH5AD.H5File | Read from and write to h5ad files
RelativeCounts | Normalize raw data to fractions
RenameCells | Rename cells
RenameCells.Assay | Rename cells
RenameCells.DimReduc | Rename cells
RenameCells.Seurat | Rename cells
RenameIdent | Get, set, and manipulate an object's identity classes
RenameIdents | Get, set, and manipulate an object's identity classes
RenameIdents.Seurat | Get, set, and manipulate an object's identity classes
ReorderIdent | Get, set, and manipulate an object's identity classes
ReorderIdent.Seurat | Get, set, and manipulate an object's identity classes
RestoreLegend | Seurat Themes
RidgePlot | Single cell ridge plot
RotatedAxis | Seurat Themes
RunALRA | Run Adaptively-thresholded Low Rank Approximation (ALRA)
RunALRA.default | Run Adaptively-thresholded Low Rank Approximation (ALRA)
RunALRA.Seurat | Run Adaptively-thresholded Low Rank Approximation (ALRA)
RunCCA | Perform Canonical Correlation Analysis
RunCCA.default | Perform Canonical Correlation Analysis
RunCCA.Seurat | Perform Canonical Correlation Analysis
RunICA | Run Independent Component Analysis on gene expression
RunICA.Assay | Run Independent Component Analysis on gene expression
RunICA.default | Run Independent Component Analysis on gene expression
RunICA.Seurat | Run Independent Component Analysis on gene expression
RunLSI | Run Latent Semantic Indexing on binary count matrix
RunLSI.Assay | Run Latent Semantic Indexing on binary count matrix
RunLSI.default | Run Latent Semantic Indexing on binary count matrix
RunLSI.Seurat | Run Latent Semantic Indexing on binary count matrix
RunPCA | Run Principal Component Analysis
RunPCA.Assay | Run Principal Component Analysis
RunPCA.default | Run Principal Component Analysis
RunPCA.Seurat | Run Principal Component Analysis
RunTSNE | Run t-distributed Stochastic Neighbor Embedding
RunTSNE.DimReduc | Run t-distributed Stochastic Neighbor Embedding
RunTSNE.dist | Run t-distributed Stochastic Neighbor Embedding
RunTSNE.matrix | Run t-distributed Stochastic Neighbor Embedding
RunTSNE.Seurat | Run t-distributed Stochastic Neighbor Embedding
RunUMAP | Run UMAP
RunUMAP.default | Run UMAP
RunUMAP.Graph | Run UMAP
RunUMAP.Seurat | Run UMAP

## -- S --

SampleUMI | Sample UMI
ScaleData | Scale and center the data.
ScaleData.Assay | Scale and center the data.
ScaleData.default | Scale and center the data.
ScaleData.Seurat | Scale and center the data.
ScoreJackStraw | Compute Jackstraw scores significance.
ScoreJackStraw.DimReduc | Compute Jackstraw scores significance.
ScoreJackStraw.JackStrawData | Compute Jackstraw scores significance.
ScoreJackStraw.Seurat | Compute Jackstraw scores significance.
SCTransform | Use regularized negative binomial regression to normalize UMI count data
SelectIntegrationFeatures | Select integration features
SetAssayData | Setter for multimodal data
SetAssayData.Assay | Setter for multimodal data
SetAssayData.Seurat | Setter for multimodal data
SetDimReduction | Create a DimReduc object
SetIdent | Get, set, and manipulate an object's identity classes
SetIdent.Seurat | Get, set, and manipulate an object's identity classes
SetIntegrationData | Set integation data
Seurat | The Seurat Class
seurat | The Seurat Class
Seurat-class | The Seurat Class
seurat-class | The Seurat Class
SeuratAccess | Add in metadata associated with either cells or features.
SeuratAxes | Seurat Themes
SeuratCommand | The SeuratCommand Class
SeuratCommand-class | The SeuratCommand Class
SeuratTheme | Seurat Themes
SpatialTheme | Seurat Themes
SplitDotPlotGG | Dot plot visualization
SplitObject | Splits object into a list of subsetted objects.
StashIdent | Get, set, and manipulate an object's identity classes
StashIdent.Seurat | Get, set, and manipulate an object's identity classes
Stdev | Get the standard deviations for an object
Stdev.DimReduc | Get the standard deviations for an object
Stdev.Seurat | Get the standard deviations for an object
StopCellbrowser | Stop Cellbrowser web server
subset | Subset a Seurat object
subset.Seurat | Subset a Seurat object
SubsetByBarcodeInflections | Subset a Seurat Object based on the Barcode Distribution Inflection Points
SubsetData | Return a subset of the Seurat object
SubsetData.Assay | Return a subset of the Seurat object
SubsetData.Seurat | Return a subset of the Seurat object

## -- T --

TF.IDF | Term frequency-inverse document frequency
Tool | Get and set additional tool data
Tool.Seurat | Get and set additional tool data
Tool<- | Get and set additional tool data
Tool<-.Seurat | Get and set additional tool data
Tools | Get and set additional tool data
TopCells | Find cells with highest scores for a given dimensional reduction technique
TopFeatures | Find features with highest scores for a given dimensional reduction technique
TransferData | Transfer Labels
TSNEPlot | Dimensional reduction plot

## -- U --

UMAPPlot | Dimensional reduction plot
UpdateSeuratObject | Update old Seurat object to accomodate new features

## -- V --

VariableFeaturePlot | View variable features
VariableFeatures | Get and set variable feature information
VariableFeatures.Assay | Get and set variable feature information
VariableFeatures.Seurat | Get and set variable feature information
VariableFeatures<- | Get and set variable feature information
VariableFeatures<-.Assay | Get and set variable feature information
VariableFeatures<-.Seurat | Get and set variable feature information
VariableGenePlot | View variable features
VizDimLoadings | Visualize Dimensional Reduction genes
VlnPlot | Single cell violin plot

## -- W --

WhichCells | Identify cells matching certain criteria
WhichCells.Assay | Identify cells matching certain criteria
WhichCells.Seurat | Identify cells matching certain criteria
WhiteBackground | Seurat Themes
WriteH5AD | Read from and write to h5ad files
WriteH5AD.Seurat | Read from and write to h5ad files

## -- misc --

[.Seurat | Subset a Seurat object
[[<--method | Add in metadata associated with either cells or features.