Man pages for atakanekiz/Seurat3.0
Tools for Single Cell Genomics

AddMetaData	Add in metadata associated with either cells or features.
AddModuleScore	Calculate module scores for featre expression programs in...
ALRAChooseKPlot	ALRA Approximate Rank Selection Plot
AnchorSet-class	The AnchorSet Class
Assay-class	The Assay Class
as.sparse	Convert between data frames and sparse matrices
AugmentPlot	Augments ggplot2-based plot with a PNG image.
AverageExpression	Averaged feature expression by identity class
BarcodeInflectionsPlot	Plot the Barcode Distribution and Calculated Inflection...
BuildClusterTree	Phylogenetic Analysis of Identity Classes
CalculateBarcodeInflections	Calculate the Barcode Distribution Inflection
CaseMatch	Match the case of character vectors
cc.genes	Cell cycle genes
CellCycleScoring	Score cell cycle phases
Cells	Get cells present in an object
CellScatter	Cell-cell scatter plot
CollapseSpeciesExpressionMatrix	Slim down a multi-species expression matrix, when only one...
CombinePlots	Combine ggplot2-based plots into a single plot
Command	Get SeuratCommands
Convert	Convert Seurat objects to other classes and vice versa
CreateAssayObject	Create an Assay object
CreateDimReducObject	Create a DimReduc object
CreateSeuratObject	Create a Seurat object
CustomDistance	Run a custom distance function on an input data matrix
CustomPalette	Create a custom color palette
DefaultAssay	Get the default assay
DietSeurat	Slim down a Seurat object
DimHeatmap	Dimensional reduction heatmap
DimPlot	Dimensional reduction plot
DimReduc-class	The Dimmensional Reduction Class
DoHeatmap	Feature expression heatmap
DotPlot	Dot plot visualization
ElbowPlot	Quickly Pick Relevant Dimensions
Embeddings	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
FeatureLocator	Feature Locator
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
FindClusters	Cluster Determination
FindConservedMarkers	Finds markers that are conserved between the two groups
FindIntegrationAnchors	Find integration anchors
FindMarkers	Gene expression markers of identity classes
FindNeighbors	SNN Graph Construction
FindTransferAnchors	Find transfer anchors
FindVariableFeatures	Find variable features
GetAssay	Get an assay from an object
GetAssayData	Accessor function for multimodal data
GetIntegrationData	Get integation data
Graph-class	The Graph Class
HoverLocator	Hover Locator
HTODemux	Demultiplex samples based on data from cell 'hashing'
HTOHeatmap	Hashtag oligo heatmap
HVFInfo	Get highly variable feature information
Idents	Get, set, and manipulate an object's identity classes
IntegrateData	Integrate data
IntegrationData-class	The IntegrationData Class
JackStraw	Determine statistical significance of PCA scores.
JackStrawData-class	The JackStrawData Class
JackStrawPlot	JackStraw Plot
JS	Get JackStraw information
Key	Get a key
L2CCA	L2-Normalize CCA
L2Dim	L2-normalization
LabelClusters	Label clusters on a ggplot2-based scatter plot
LabelPoints	Add text labels to a ggplot2 plot
Loadings	Get feature loadings
LocalStruct	Calculate the local structure preservation metric
LogNormalize	Normalize raw data
LogVMR	Calculate the variance to mean ratio of logged values
merge.Seurat	Merge Seurat Objects
MetaFeature	Aggregate expression of multiple features into a single...
MinMax	Apply a ceiling and floor to all values in a matrix
Misc	Access miscellaneous data
MixingMetric	Calculates a mixing metric
NormalizeData	Normalize Data
oldseurat-class	The Seurat Class
OldWhichCells	Identify cells matching certain criteria
pbmc_small	A small example version of the PBMC dataset
PCASigGenes	Significant genes from a PCA
PolyDimPlot	Polygon DimPlot
PolyFeaturePlot	Polygon FeaturePlot
print.DimReduc	Print the results of a dimensional reduction analysis
ProjectDim	Project Dimensional reduction onto full dataset
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
RegressRegNB	Use regularized negative binomial regression to normalize UMI...
RelativeCounts	Normalize raw data to fractions
RenameCells	Rename cells
RidgePlot	Single cell ridge plot
RunALRA	Run Adaptively-thresholded Low Rank Approximation (ALRA)
RunCCA	Perform Canonical Correlation Analysis
RunICA	Run Independent Component Analysis on gene expression
RunPCA	Run Principal Component Analysis
RunTSNE	Run t-distributed Stochastic Neighbor Embedding
RunUMAP	Run UMAP
SampleUMI	Sample UMI
ScaleData	Scale and center the data.
ScoreJackStraw	Compute Jackstraw scores significance.
SelectIntegrationFeatures	Select integration features
SetAssayData	Setter for multimodal data
SetIntegrationData	Set integation data
Seurat-class	The Seurat Class
SeuratCommand-class	The SeuratCommand Class
SeuratTheme	Seurat Themes
SplitObject	Splits object into a list of subsetted objects.
Stdev	Get the standard deviations for an object
StopCellbrowser	Stop Cellbrowser web server
SubsetByBarcodeInflections	Subset a Seurat Object based on the Barcode Distribution...
SubsetData	Return a subset of the Seurat object
subset.Seurat	Subset a Seurat object
Tool	Get and set additional tool data
TopCells	Find cells with highest scores for a given dimensional...
TopFeatures	Find features with highest scores for a given dimensional...
TransferData	Transfer Labels
UpdateSeuratObject	Update old Seurat object to accomodate new features
VariableFeaturePlot	View variable features
VariableFeatures	Get and set variable feature information
VizDimLoadings	Visualize Dimensional Reduction genes
VlnPlot	Single cell violin plot
WhichCells	Identify cells matching certain criteria