Man pages for Seurat
Tools for Single Cell Genomics

AddMetaDataAdd in metadata associated with either cells or features.
AddModuleScoreCalculate module scores for feature expression programs in...
ALRAChooseKPlotALRA Approximate Rank Selection Plot
AnchorSet-classThe AnchorSet Class
as.CellDataSetConvert objects to CellDataSet objects
as.GraphConvert a matrix (or Matrix) to the Graph class.
as.list.SeuratCommandCoerce a SeuratCommand to a list
as.loomConvert objects to loom objects
as.NeighborConvert objects to Neighbor ojbects
Assay-classThe Assay Class
AssaysPull Assays or assay names
as.SeuratConvert objects to Seurat objects
as.SingleCellExperimentConvert objects to SingleCellExperiment objects
as.sparseConvert between data frames and sparse matrices
AugmentPlotAugments ggplot2-based plot with a PNG image.
AverageExpressionAveraged feature expression by identity class
BarcodeInflectionsPlotPlot the Barcode Distribution and Calculated Inflection...
BGTextColorDetermine text color based on background color
BuildClusterTreePhylogenetic Analysis of Identity Classes
CalculateBarcodeInflectionsCalculate the Barcode Distribution Inflection
CaseMatchMatch the case of character vectors
cc.genesCell cycle genes
cc.genes.updated.2019Cell cycle genes: 2019 update
CellCycleScoringScore cell cycle phases
CellsGet cells present in an object
CellsByIdentitiesGet cell names grouped by identity class
CellsByImageGet a vector of cell names associated with an image (or set...
CellScatterCell-cell scatter plot
CellSelectorCell Selector
CollapseEmbeddingOutliersMove outliers towards center on dimension reduction plot
CollapseSpeciesExpressionMatrixSlim down a multi-species expression matrix, when only one...
ColorDimSplitColor dimensional reduction plot by tree split
CombinePlotsCombine ggplot2-based plots into a single plot
CommandGet SeuratCommands
contrast-theoryGet the intensity and/or luminance of a color
CreateAssayObjectCreate an Assay object
CreateDimReducObjectCreate a DimReduc object
CreateGeneActivityMatrixConvert a peak matrix to a gene activity matrix
CreateSeuratObjectCreate a 'Seurat' object
CustomDistanceRun a custom distance function on an input data matrix
CustomPaletteCreate a custom color palette
DefaultAssayGet and set the default assay
DietSeuratSlim down a Seurat object
DimHeatmapDimensional reduction heatmap
DimPlotDimensional reduction plot
DimReduc-classThe Dimmensional Reduction Class
DiscretePaletteDiscrete colour palettes from the pals package
DistancesGet the Neighbor nearest neighbors distance matrix
DoHeatmapFeature expression heatmap
DotPlotDot plot visualization
ElbowPlotQuickly Pick Relevant Dimensions
EmbeddingsGet cell embeddings
ExpMeanCalculate the mean of logged values
ExportToCellbrowserExport Seurat object for UCSC cell browser
ExpSDCalculate the standard deviation of logged values
ExpVarCalculate the variance of logged values
FastRowScaleScale and/or center matrix rowwise
FeaturePlotVisualize 'features' on a dimensional reduction plot
FeatureScatterScatter plot of single cell data
FetchDataAccess cellular data
FilterSlideSeqFilter stray beads from Slide-seq puck
FindAllMarkersGene expression markers for all identity classes
FindClustersCluster Determination
FindConservedMarkersFinds markers that are conserved between the groups
FindIntegrationAnchorsFind integration anchors
FindMarkersGene expression markers of identity classes
FindNeighborsSNN Graph Construction
FindSpatiallyVariableFeaturesFind spatially variable features
FindTransferAnchorsFind transfer anchors
FindVariableFeaturesFind variable features
GetAssayGet an Assay object from a given Seurat object.
GetAssayDataGeneral accessor function for the Assay class
GetImageGet image data
GetIntegrationDataGet integation data
GetResidualCalculate pearson residuals of features not in the scale.data
GetTissueCoordinatesGet tissue coordinates
GetTransferPredictionsGet the predicted identity
Graph-classThe Graph Class
GroupCorrelationCompute the correlation of features broken down by groups...
GroupCorrelationPlotBoxplot of correlation of a variable (e.g. number of UMIs)...
h5adRead from and write to h5ad files
HoverLocatorHover Locator
HTODemuxDemultiplex samples based on data from cell 'hashing'
HTOHeatmapHashtag oligo heatmap
HVFInfoGet highly variable feature information
IdentsGet, set, and manipulate an object's identity classes
IFeaturePlotVisualize features in dimensional reduction space...
ImagesPull spatial image names
IndexGet Neighbor algorithm index
IndicesGet Neighbor nearest neighbor index matrices
IntegrateDataIntegrate data
IntegrationData-classThe IntegrationData Class
IsGlobalIs an object global/persistent?
ISpatialDimPlotVisualize clusters spatially and interactively
ISpatialFeaturePlotVisualize features spatially and interactively
JackStrawDetermine statistical significance of PCA scores.
JackStrawData-classThe JackStrawData Class
JackStrawPlotJackStraw Plot
JSGet JackStraw information
KeyGet a key
L2CCAL2-Normalize CCA
L2DimL2-normalization
LabelClustersLabel clusters on a ggplot2-based scatter plot
LabelPointsAdd text labels to a ggplot2 plot
LinkedPlotsVisualize spatial and clustering (dimensional reduction) data...
Load10X_SpatialLoad a 10x Genomics Visium Spatial Experiment into a 'Seurat'...
LoadAnnoyIndexLoad the Annoy index file
LoadingsGet feature loadings
LoadSTARmapLoad STARmap data
LocalStructCalculate the local structure preservation metric
LogNormalizeNormalize raw data
LogSeuratCommandLog a command
LogVMRCalculate the variance to mean ratio of logged values
merge.SeuratMerge Seurat Objects
MetaFeatureAggregate expression of multiple features into a single...
MinMaxApply a ceiling and floor to all values in a matrix
MiscAccess miscellaneous data
MixingMetricCalculates a mixing metric
MULTIseqDemuxDemultiplex samples based on classification method from...
Neighbor-classThe Neighbor class
NeighborsPull Neighbor or Neighbor names
NormalizeDataNormalize Data
oldseurat-classThe Seurat Class
OldWhichCellsIdentify cells matching certain criteria
pbmc_smallA small example version of the PBMC dataset
PCASigGenesSignificant genes from a PCA
PercentageFeatureSetCalculate the percentage of all counts that belong to a given...
PlotClusterTreePlot clusters as a tree
PolyDimPlotPolygon DimPlot
PolyFeaturePlotPolygon FeaturePlot
PrepSCTIntegrationPrepare an object list normalized with sctransform for...
print.DimReducPrint the results of a dimensional reduction analysis
ProjectGet and set project information
ProjectDimProject Dimensional reduction onto full dataset
RadiusGet the spot radius from an image
Read10XLoad in data from 10X
Read10X_h5Read 10X hdf5 file
Read10X_ImageLoad a 10X Genomics Visium Image
ReadAlevinLoad in data from Alevin pipeline
ReadAlevinCsvLoad in data from Alevin pipeline
ReadSlideSeqLoad Slide-seq spatial data
ReductionsPull DimReducs or DimReduc names
RegroupIdentsRegroup idents based on meta.data info
RelativeCountsNormalize raw data to fractions
RenameAssaysRename assays in a 'Seurat' object
RenameCellsRename cells
RidgePlotSingle cell ridge plot
RowMergeSparseMatricesMerge two matrices by rowname
RunALRARun Adaptively-thresholded Low Rank Approximation (ALRA)
RunCCAPerform Canonical Correlation Analysis
RunICARun Independent Component Analysis on gene expression
RunLSIRun Latent Semantic Indexing on binary count matrix
RunMarkVarioRun the mark variogram computation on a given position matrix...
RunMoransICompute Moran's I value.
RunPCARun Principal Component Analysis
RunTSNERun t-distributed Stochastic Neighbor Embedding
RunUMAPRun UMAP
SampleUMISample UMI
SaveAnnoyIndexSave the Annoy index
ScaleDataScale and center the data.
ScaleFactorsGet image scale factors
ScoreJackStrawCompute Jackstraw scores significance.
SCTransformUse regularized negative binomial regression to normalize UMI...
SelectIntegrationFeaturesSelect integration features
SetAssayDataSetter for multimodal data
SetIntegrationDataSet integation data
Seurat-classThe Seurat Class
SeuratCommand-classThe SeuratCommand Class
Seurat-packageSeurat package
SeuratThemeSeurat Themes
SlideSeq-classThe SlideSeq class
SpatialImage-classThe SpatialImage class
SpatiallyVariableFeaturesGet spatially variable feature information
SpatialPlotVisualize spatial clustering and expression data.
SplitObjectSplits object into a list of subsetted objects.
STARmap-classThe STARmap class
StdevGet the standard deviations for an object
StopCellbrowserStop Cellbrowser web server
SubsetByBarcodeInflectionsSubset a Seurat Object based on the Barcode Distribution...
SubsetDataReturn a subset of the Seurat object
subset.SeuratSubset a Seurat object
SVFInfoGet spatially variable feature information
TF.IDFTerm frequency-inverse document frequency
ToolGet and set additional tool data
TopCellsFind cells with highest scores for a given dimensional...
TopFeaturesFind features with highest scores for a given dimensional...
TopNeighborsGet nearest neighbors for given cell
TransferDataTransfer data
UpdateSeuratObjectUpdate old Seurat object to accomodate new features
UpdateSymbolListGet updated synonyms for gene symbols
VariableFeaturePlotView variable features
VariableFeaturesGet and set variable feature information
VisiumV1-classThe VisiumV1 class
VizDimLoadingsVisualize Dimensional Reduction genes
VlnPlotSingle cell violin plot
WhichCellsIdentify cells matching certain criteria
Seurat documentation built on Jan. 13, 2021, 7:11 p.m.