Man pages for Seurat
Tools for Single Cell Genomics

AddImputedScoreCalculate imputed expression values
AddMetaDataAdd Metadata
AddModuleScoreCalculate module scores for gene expression programs in...
AddSamplesAdd samples into existing Seurat object.
AddSmoothedScoreCalculate smoothed expression values
AlignSubspaceAlign subspaces using dynamic time warping (DTW)
AssessNodesAssess Internal Nodes
AssessSplitAssess Cluster Split
AverageDetectionRateProbability of detection by identity class
AverageExpressionAveraged gene expression by identity class
AveragePCAAverage PCA scores by identity class
BlackAndWhiteA black and white color palette
BuildClusterTreePhylogenetic Analysis of Identity Classes
BuildRFClassifierBuild Random Forest Classifier
BuildSNNSNN Graph Construction
CalcAlignmentMetricCalculate an alignment score
CalcVarExpRatioCalculate the ratio of variance explained by ICA or PCA to...
CaseMatchMatch the case of character vectors
cc.genesCell cycle genes
CellCycleScoringScore cell cycle phases
CellPlotCell-cell scatter plot
ClassifyCellsClassify New Data
CollapseSpeciesExpressionMatrixSlim down a multi-species expression matrix, when only one...
ColorTSNESplitColor tSNE Plot Based on Split
CreateSeuratObjectInitialize and setup the Seurat object
CustomDistanceRun a custom distance function on an input data matrix
CustomPaletteCreate a custom color palette
DarkThemeDark Theme
DBClustDimensionPerform spectral density clustering on single cells
DESeq2DETestDifferential expression using DESeq2
DiffExpTestLikelihood ratio test for zero-inflated data
DiffTTestDifferential expression testing using Student's t-test
DimElbowPlotQuickly Pick Relevant Dimensions
DimHeatmapDimensional reduction heatmap
DimPlotDimensional reduction plot
DimTopCellsFind cells with highest scores for a given dimensional...
DimTopGenesFind genes with highest scores for a given dimensional...
DMEmbedDiffusion Maps Cell Embeddings Accessor Function
DMPlotPlot Diffusion map
DoHeatmapGene expression heatmap
DoKMeansK-Means Clustering
DotPlotDot plot visualization
DotPlotOldOld Dot plot visualization (pre-ggplot implementation)...
ExpMeanCalculate the mean of logged values
ExpSDCalculate the standard deviation of logged values
ExpVarCalculate the variance of logged values
ExtractFieldExtract delimiter information from a string.
FastWhichCellsFastWhichCells Identify cells matching certain criteria...
FeatureHeatmapVizualization of multiple features
FeatureLocatorFeature Locator
FeaturePlotVisualize 'features' on a dimensional reduction plot
FetchDataAccess cellular data
FilterCellsReturn a subset of the Seurat object
FindAllMarkersGene expression markers for all identity classes
FindAllMarkersNodeFind all markers for a node
FindClustersCluster Determination
FindConservedMarkersFinds markers that are conserved between the two groups
FindMarkersGene expression markers of identity classes
FindMarkersNodeGene expression markers of identity classes defined by a...
FindVariableGenesIdentify variable genes
FitGeneKBuild mixture models of gene expression
GenePlotScatter plot of single cell data
GetAssayDataAccessor function for multimodal data
GetCellEmbeddingsDimensional Reduction Cell Embeddings Accessor Function
GetCentroidsGet cell centroids
GetClustersGet Cluster Assignments
GetDimReductionDimensional Reduction Accessor Function
GetGeneLoadingsDimensional Reduction Gene Loadings Accessor Function
HoverLocatorHover Locator
ICAEmbedICA Cell Embeddings Accessor Function
ICALoadICA Gene Loadings Accessor Function
ICAPlotPlot ICA map
ICHeatmapIndependent component heatmap
ICTopCellsFind cells with highest ICA scores
ICTopGenesFind genes with highest ICA scores
InitialMappingInfer spatial origins for single cells
JackStrawDetermine statistical significance of PCA scores.
JackStrawPlotJackStraw Plot
KClustDimensionPerform spectral k-means clustering on single cells
KMeansHeatmapPlot k-means clusters
LogNormalizeNormalize raw data
LogVMRCalculate the variance to mean ratio of logged values
MakeSparseMake object sparse
MarkerTestROC-based marker discovery
MASTDETestDifferential expression using MAST
MatrixRowShuffleIndependently shuffle values within each row of a matrix
MergeNodeMerge childen of a node
MergeSeuratMerge Seurat Objects
MetageneBicorPlotPlot CC bicor saturation plot
MinMaxApply a ceiling and floor to all values in a matrix
NegBinomDETestNegative binomial test for UMI-count based data
NegBinomRegDETestNegative binomial test for UMI-count based data (regularized...
NormalizeDataNormalize Assay Data
NumberClustersConvert the cluster labels to a numeric representation
OldDoHeatmapGene expression heatmap
pbmc_smallA small example version of the PBMC dataset
PCAEmbedPCA Cell Embeddings Accessor Function
PCALoadPCA Gene Loadings Accessor Function
PCAPlotPlot PCA map
PCASigGenesSignificant genes from a PCA
PCElbowPlotQuickly Pick Relevant PCs
PCHeatmapPrincipal component heatmap
PCTopCellsFind cells with highest PCA scores
PCTopGenesFind genes with highest PCA scores
PlotClusterTreePlot phylogenetic tree
PoissonDETestPoisson test for UMI-count based data
PrintAlignSubspaceParamsPrint AlignSubspace Calculation Parameters
PrintCalcParamsPrint the calculation
PrintCalcVarExpRatioParamsPrint Parameters Associated with CalcVarExpRatio
PrintCCAParamsPrint CCA Calculation Parameters
PrintDimPrint the results of a dimensional reduction analysis
PrintDMParamsPrint Diffusion Map Calculation Parameters
PrintFindClustersParamsPrint FindClusters Calculation Parameters
PrintICAPrint the results of a ICA analysis
PrintICAParamsPrint ICA Calculation Parameters
PrintPCAPrint the results of a PCA analysis
PrintPCAParamsPrint PCA Calculation Parameters
PrintSNNParamsPrint SNN Construction Calculation Parameters
PrintTSNEParamsPrint TSNE Calculation Parameters
ProjectDimProject Dimensional reduction onto full dataset
ProjectPCAProject Principal Components Analysis onto full dataset
PurpleAndYellowA purple and yellow color palette
Read10XLoad in data from 10X
RefinedMappingQuantitative refinement of spatial inferences
RemoveFromTableRemove data from a table
RenameIdentRename one identity class to another
ReorderIdentReorder identity classes
RidgePlotSingle cell ridge plot
RunCCAPerform Canonical Correlation Analysis
RunDiffusionRun diffusion map
RunICARun Independent Component Analysis on gene expression
RunMultiCCAPerform Canonical Correlation Analysis with more than two...
RunPCARun Principal Component Analysis on gene expression using...
RunTSNERun t-distributed Stochastic Neighbor Embedding
SampleUMISample UMI
SaveClustersSave cluster assignments to a TSV file
ScaleDataScale and center the data.
ScaleDataROld R based implementation of ScaleData. Scales and centers...
SetAllIdentSwitch identity class definition to another variable
SetAssayDataAssay Data Mutator Function
SetClustersSet Cluster Assignments
SetDimReductionDimensional Reduction Mutator Function
SetIdentSet identity class information
seuratThe Seurat Class
Seurat-deprecatedDeprecated function(s) in the Seurat package
show-methodsshow method for seurat
ShuffleShuffle a vector
SplitDotPlotGGSplit Dot plot visualization
StashIdentSet identity class information
SubsetColumnReturn a subset of columns for a matrix or data frame
SubsetDataReturn a subset of the Seurat object
SubsetRowReturn a subset of rows for a matrix or data frame
TobitTestDifferential expression testing using Tobit models
TSNEPlotPlot tSNE map
UpdateSeuratObjectUpdate old Seurat object to accomodate new features
ValidateClustersCluster Validation
ValidateSpecificClustersSpecific Cluster Validation
VariableGenePlotView variable genes
VizDimReductionVisualize Dimensional Reduction genes
VizICAVisualize ICA genes
VizPCAVisualize PCA genes
VlnPlotSingle cell violin plot
WhichCellsIdentify cells matching certain criteria
WilcoxDETestDifferential expression using Wilcoxon Rank Sum
Seurat documentation built on Feb. 15, 2018, 1:01 a.m.