Man pages for Seurat
Tools for Single Cell Genomics

AddAzimuthResultsAdd Azimuth Results
AddAzimuthScoresAdd Azimuth Scores
AddModuleScoreCalculate module scores for feature expression programs in...
AggregateExpressionAggregated feature expression by identity class
AnchorSet-classThe AnchorSet Class
AnnotateAnchorsAdd info to anchor matrix
as.CellDataSetConvert objects to CellDataSet objects
Assay-classThe Assay Class
as.SeuratConvert objects to 'Seurat' objects
as.SingleCellExperimentConvert objects to SingleCellExperiment objects
as.sparseCast to Sparse
AugmentPlotAugments ggplot2-based plot with a PNG image.
AutoPointSizeAutomagically calculate a point size for ggplot2-based...
AverageExpressionAveraged feature expression by identity class
BarcodeInflectionsPlotPlot the Barcode Distribution and Calculated Inflection...
BGTextColorDetermine text color based on background color
BridgeCellsRepresentationConstruct a dictionary representation for each unimodal...
BridgeReferenceSet-classThe BridgeReferenceSet Class The BridgeReferenceSet is an...
BuildClusterTreePhylogenetic Analysis of Identity Classes
BuildNicheAssayConstruct an assay for spatial niche analysis
CalcDispersionCalculate dispersion of features
CalcPerturbSigCalculate a perturbation Signature
CalculateBarcodeInflectionsCalculate the Barcode Distribution Inflection
CaseMatchMatch the case of character vectors
CCAIntegrationSeurat-CCA Integration
cc.genesCell cycle genes
cc.genes.updated.2019Cell cycle genes: 2019 update
CellCycleScoringScore cell cycle phases
CellsGet Cell Names
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
contrast-theoryGet the intensity and/or luminance of a color
CountSketchGenerate CountSketch random matrix
CreateCategoryMatrixCreate one hot matrix for a given label
CreateSCTAssayObjectCreate a SCT Assay object
CustomDistanceRun a custom distance function on an input data matrix
CustomPaletteCreate a custom color palette
DEenrichRPlotDE and EnrichR pathway visualization barplot
DietSeuratSlim down a Seurat object
DimHeatmapDimensional reduction heatmap
DimPlotDimensional reduction plot
DimReduc-classThe DimReduc Class
DiscretePaletteDiscrete colour palettes from pals
DISPFind variable features based on dispersion
DoHeatmapFeature expression heatmap
DotPlotDot plot visualization
ElbowPlotQuickly Pick Relevant Dimensions
ExpMeanCalculate the mean of logged values
ExpSDCalculate the standard deviation of logged values
ExpVarCalculate the variance of logged values
FastRowScaleScale and/or center matrix rowwise
FastRPCAIntegrationPerform integration on the joint PCA cell embeddings.
FeaturePlotVisualize 'features' on a dimensional reduction plot
FeatureScatterScatter plot of single cell data
FetchResidualsCalculate pearson residuals of features not in the
FetchResidualSCTModelCalculate pearson residuals of features not in the
FetchResiduals_referencetemporal function to get residuals from reference
FilterSlideSeqFilter stray beads from Slide-seq puck
FindAllMarkersGene expression markers for all identity classes
FindBridgeAnchorFind bridge anchors between two unimodal datasets
FindBridgeIntegrationAnchorsFind integration bridge anchors between query and extended...
FindBridgeTransferAnchorsFind bridge anchors between query and extended...
FindClustersCluster Determination
FindConservedMarkersFinds markers that are conserved between the groups
FindIntegrationAnchorsFind integration anchors
FindMarkersGene expression markers of identity classes
FindMultiModalNeighborsConstruct weighted nearest neighbor graph
FindNeighbors(Shared) Nearest-neighbor graph construction
FindSpatiallyVariableFeaturesFind spatially variable features
FindSubClusterFind subclusters under one cluster
FindTransferAnchorsFind transfer anchors
FindVariableFeaturesFind variable features
FoldChangeFold Change
fortify-SpatialPrepare Coordinates for Spatial Plots
GaussianSketchGaussian sketching
GetAssayGet an Assay object from a given Seurat object.
GetImageGet Image Data
GetIntegrationDataGet integration data
GetResidualCalculate pearson residuals of features not in the
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)...
HarmonyIntegrationHarmony Integration
HoverLocatorHover Locator
HTODemuxDemultiplex samples based on data from cell 'hashing'
HTOHeatmapHashtag oligo heatmap
HVFInfo.SCTAssayGet Variable Feature Information
IFeaturePlotVisualize features in dimensional reduction space...
ImageDimPlotSpatial Cluster Plots
ImageFeaturePlotSpatial Feature Plots
IntegrateDataIntegrate data
IntegrateEmbeddingsIntegrate low dimensional embeddings
IntegrateLayersIntegrate Layers
IntegrationAnchorSet-classThe IntegrationAnchorSet Class
IntegrationData-classThe IntegrationData Class
ISpatialDimPlotVisualize clusters spatially and interactively
ISpatialFeaturePlotVisualize features spatially and interactively
JackStrawDetermine statistical significance of PCA scores.
JackStrawData-classThe JackStrawData Class
JackStrawPlotJackStraw Plot
JointPCAIntegrationSeurat-Joint PCA Integration
L2CCAL2-Normalize CCA
LabelClustersLabel clusters on a ggplot2-based scatter plot
LabelPointsAdd text labels to a ggplot2 plot
LeverageScoreLeverage Score Calculation
LinkedPlotsVisualize spatial and clustering (dimensional reduction) data...
Load10X_SpatialLoad a 10x Genomics Visium Spatial Experiment into a 'Seurat'...
LoadAnnoyIndexLoad the Annoy index file
LoadCurioSeekerLoad Curio Seeker data
LoadSTARmapLoad STARmap data
LocalStructCalculate the local structure preservation metric
LogNormalizeNormalize Raw Data
LogVMRCalculate the variance to mean ratio of logged values
MappingScoreMetric for evaluating mapping success
MapQueryMap query cells to a reference
merge.SCTAssayMerge SCTAssay objects
MetaFeatureAggregate expression of multiple features into a single...
MinMaxApply a ceiling and floor to all values in a matrix
MixingMetricCalculates a mixing metric
MixscapeHeatmapDifferential expression heatmap for mixscape
MixscapeLDALinear discriminant analysis on pooled CRISPR screen data.
ModalityWeights-classThe ModalityWeights Class
MULTIseqDemuxDemultiplex samples based on classification method from...
MVPFind variable features based on mean.var.plot
Neighbor-classThe Neighbor Class
NNPlotHighlight Neighbors in DimPlot
NNtoGraphConvert Neighbor class to an asymmetrical Graph class
NormalizeDataNormalize Data
PCASigGenesSignificant genes from a PCA
PercentAboveCalculate the percentage of a vector above some threshold
PercentageFeatureSetCalculate the percentage of all counts that belong to a given...
PlotClusterTreePlot clusters as a tree
PlotPerturbScoreFunction to plot perturbation score distributions.
PolyDimPlotPolygon DimPlot
PolyFeaturePlotPolygon FeaturePlot
PredictAssayPredict value from nearest neighbors
PrepareBridgeReferencePrepare the bridge and reference datasets
PrepLDAFunction to prepare data for Linear Discriminant Analysis.
PrepSCTFindMarkersPrepare object to run differential expression on SCT assay...
PrepSCTIntegrationPrepare an object list normalized with sctransform for...
ProjectCellEmbeddingsProject query data to the reference dimensional reduction
ProjectDataProject full data to the sketch assay
ProjectDimProject Dimensional reduction onto full dataset
ProjectDimReducProject query data to reference dimensional reduction
ProjectIntegrationIntegrate embeddings from the integrated sketched.assay
ProjectUMAPProject query into UMAP coordinates of a reference
PseudobulkExpressionPseudobulk Expression
RadiusGet Spot Radius
Read10XLoad in data from 10X
Read10X_h5Read 10X hdf5 file
Read10X_ImageLoad a 10X Genomics Visium Image
Read10X_probe_metadataRead10x Probe Metadata
ReadAkoyaRead and Load Akoya CODEX data
ReadMtxLoad in data from remote or local mtx files
ReadNanostringRead and Load Nanostring SMI data
ReadParseBioRead output from Parse Biosciences
ReadSlideSeqLoad Slide-seq spatial data
ReadSTARsoloRead output from STARsolo
ReadVitessceRead Data From Vitessce
ReadVizgenRead and Load MERFISH Input from Vizgen
ReadXeniumRead and Load 10x Genomics Xenium in-situ data
reexportsObjects exported from other packages
RegroupIdentsRegroup idents based on info
RelativeCountsNormalize raw data to fractions
RenameCellsRename Cells in an Object
RidgePlotSingle cell ridge plot
RPCAIntegrationSeurat-RPCA Integration
RunCCAPerform Canonical Correlation Analysis
RunGraphLaplacianRun Graph Laplacian Eigendecomposition
RunICARun Independent Component Analysis on gene expression
RunLDARun Linear Discriminant Analysis
RunMarkVarioRun the mark variogram computation on a given position matrix...
RunMixscapeRun Mixscape
RunMoransICompute Moran's I value.
RunPCARun Principal Component Analysis
RunSLSIRun Supervised Latent Semantic Indexing
RunSPCARun Supervised Principal Component Analysis
RunTSNERun t-distributed Stochastic Neighbor Embedding
SampleUMISample UMI
SaveAnnoyIndexSave the Annoy index
ScaleDataScale and center the data.
ScaleFactorsGet image scale factors
ScoreJackStrawCompute Jackstraw scores significance.
SCTAssay-classThe SCTModel Class
SCTransformPerform sctransform-based normalization
SCTResultsGet SCT results from an Assay
SelectIntegrationFeaturesSelect integration features
SelectIntegrationFeatures5Select integration features
SelectSCTIntegrationFeaturesSelect SCT integration features
SetIntegrationDataSet integration data
SetQuantileFind the Quantile of Data
Seurat-classThe Seurat Class
SeuratCommand-classThe SeuratCommand Class
Seurat-packageSeurat: Tools for Single Cell Genomics
SeuratThemeSeurat Themes
SingleCorPlotA single correlation plot
SingleDimPlotPlot a single dimension
SingleExIPlotPlot a single expression by identity on a plot
SingleImageMapA single heatmap from base R using 'image'
SingleImagePlotSingle Spatial Plot
SingleRasterMapA single heatmap from ggplot2 using geom_raster
SingleSpatialPlotBase plotting function for all Spatial plots
SketchDataSketch Data
SlideSeq-classThe SlideSeq class
SpatialImage-classThe SpatialImage Class
SpatialPlotVisualize spatial clustering and expression data.
SplitObjectSplits object into a list of subsetted objects.
STARmap-classThe STARmap class
subset.AnchorSetSubset an AnchorSet object
SubsetByBarcodeInflectionsSubset a Seurat Object based on the Barcode Distribution...
TopCellsFind cells with highest scores for a given dimensional...
TopFeaturesFind features with highest scores for a given dimensional...
TopNeighborsGet nearest neighbors for given cell
TransferAnchorSet-classThe TransferAnchorSet Class
TransferDataTransfer data
TransferSketchLabelsTransfer data from sketch data to full data
UnSketchEmbeddingsTransfer embeddings from sketched cells to the full data
UpdateSCTAssaysUpdate pre-V4 Assays generated with SCTransform in the Seurat...
UpdateSymbolListGet updated synonyms for gene symbols
VariableFeaturePlotView variable features
VisiumV1-classThe VisiumV1 class
VizDimLoadingsVisualize Dimensional Reduction genes
VlnPlotSingle cell violin plot
VSTVariance Stabilizing Transformation
writing-integrationWriting Integration Method Functions
Seurat documentation built on Nov. 18, 2023, 1:10 a.m.