# Seurat : R toolkit for single cell genomics

## Documentation for package ‘Seurat’ version 1.4.0.16

- DESCRIPTION file.

## Help Pages

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

## -- A --

AddImputedScore | Calculate imputed expression values
addImputedScore | Deprecated function(s) in the Seurat package
AddMetaData | Add Metadata
addMetaData | Deprecated function(s) in the Seurat package
AddSamples | Add samples into existing Seurat object.
AddSmoothedScore | Calculate smoothed expression values
addSmoothedScore | Deprecated function(s) in the Seurat package
add_samples | Deprecated function(s) in the Seurat package
AssessNodes | Assess Internal Nodes
AssessSplit | Assess Cluster Split
average.expression | Deprecated function(s) in the Seurat package
average.pca | Deprecated function(s) in the Seurat package
AverageExpression | Averaged gene expression by identity class
AveragePCA | Average PCA scores by identity class

## -- B --

batch.gene | Deprecated function(s) in the Seurat package
BatchGene | Identify potential genes associated with batch effects
BuildClusterTree | Phylogenetic Analysis of Identity Classes
buildClusterTree | Deprecated function(s) in the Seurat package
BuildRFClassifier | Build Random Forest Classifier
BuildSNN | SNN Graph Construction

## -- C --

calc.insitu | Deprecated function(s) in the Seurat package
calcNoiseModels | Deprecated function(s) in the Seurat package
calinskiPlot | Deprecated function(s) in the Seurat package
cell.cor.matrix | Deprecated function(s) in the Seurat package
CellPlot | Cell-cell scatter plot
cellPlot | Deprecated function(s) in the Seurat package
ClassifyCells | Classify New Data
cluster.alpha | Deprecated function(s) in the Seurat package
ClusterAlpha | Probability of detection by identity class
ColorTSNESplit | Color tSNE Plot Based on Split

## -- D --

DBClustDimension | Perform spectral density clustering on single cells
DBclust_dimension | Deprecated function(s) in the Seurat package
diff.t.test | Deprecated function(s) in the Seurat package
diffExp.test | Deprecated function(s) in the Seurat package
DiffExpTest | Likelihood ratio test for zero-inflated data
DiffTTest | Differential expression testing using Student's t-test
dim.plot | Deprecated function(s) in the Seurat package
DimPlot | Dimensional reduction plot
DoHeatmap | Gene expression heatmap
doHeatMap | Deprecated function(s) in the Seurat package
DoKMeans | K-Means Clustering
doKMeans | Deprecated function(s) in the Seurat package
dot.plot | Deprecated function(s) in the Seurat package
DotPlot | Dot plot visualization

## -- F --

feature.heatmap | Deprecated function(s) in the Seurat package
feature.plot | Deprecated function(s) in the Seurat package
feature.plot.keynote | Deprecated function(s) in the Seurat package
FeatureHeatmap | Vizualization of multiple features
FeaturePlot | Visualize 'features' on a dimensional reduction plot
fetch.data | Deprecated function(s) in the Seurat package
FetchData | Access cellular data
find.markers | Deprecated function(s) in the Seurat package
find.markers.node | Deprecated function(s) in the Seurat package
FindAllMarkers | Gene expression markers for all identity classes
FindAllMarkersNode | Find all markers for a node
FindClusters | Cluster Determination
FindMarkers | Gene expression markers of identity classes
FindMarkersNode | Gene expression markers of identity classes defined by a phylogenetic clade
find_all_markers | Deprecated function(s) in the Seurat package
fit.gene.k | Deprecated function(s) in the Seurat package
fit.gene.mix | Deprecated function(s) in the Seurat package
FitGeneK | Build mixture models of gene expression

## -- G --

gene.cor.matrix | Deprecated function(s) in the Seurat package
GenePlot | Scatter plot of single cell data
genePlot | Deprecated function(s) in the Seurat package
genes.in.cluster | Deprecated function(s) in the Seurat package
geneScorePlot | Deprecated function(s) in the Seurat package
get.centroids | Deprecated function(s) in the Seurat package
GetCentroids | Get cell centroids
getNewScore | Deprecated function(s) in the Seurat package
getWeightMatrix | Deprecated function(s) in the Seurat package

## -- H --

HeatmapNode | Node Heatmap

## -- I --

ICA | Run Independent Component Analysis on gene expression
ica | Deprecated function(s) in the Seurat package
ica.plot | Deprecated function(s) in the Seurat package
ICAPlot | Plot ICA map
ICHeatmap | Independent component heatmap
icHeatmap | Deprecated function(s) in the Seurat package
ICTopGenes | Find genes with highest ICA scores
icTopGenes | Deprecated function(s) in the Seurat package
initial.mapping | Deprecated function(s) in the Seurat package
InitialMapping | Infer spatial origins for single cells

## -- J --

JackStraw | Determine statistical significance of PCA scores.
jackStraw | Deprecated function(s) in the Seurat package
jackStraw.permutation.test | Deprecated function(s) in the Seurat package
jackStrawFull | Deprecated function(s) in the Seurat package
jackStrawMC | Deprecated function(s) in the Seurat package
JackStrawPlot | JackStraw Plot
jackStrawPlot | Deprecated function(s) in the Seurat package

## -- K --

KClustDimension | Perform spectral k-means clustering on single cells
Kclust_dimension | Deprecated function(s) in the Seurat package
kMeansHeatmap | Deprecated function(s) in the Seurat package

## -- L --

LogNormalize | Normalize raw data

## -- M --

MakeSparse | Make object sparse
map.cell | Deprecated function(s) in the Seurat package
marker.test | Deprecated function(s) in the Seurat package
MarkerTest | ROC-based marker discovery
mean.var.plot | Deprecated function(s) in the Seurat package
MeanVarPlot | Identify variable genes
MergeNode | Merge subchilden of a node
MergeSeurat | Merge Seurat Objects

## -- N --

NegBinomDETest | Negative binomial test for UMI-count based data

## -- P --

PCA | Run Principal Component Analysis on gene expression
pca | Deprecated function(s) in the Seurat package
pca.plot | Deprecated function(s) in the Seurat package
pca.sig.genes | Deprecated function(s) in the Seurat package
PCAFast | Run Principal Component Analysis on gene expression using IRLBA
PCAPlot | Plot PCA map
PCASigGenes | Significant genes from a PCA
PCElbowPlot | Quickly Pick Relevant PCs
PCHeatmap | Principal component heatmap
pcHeatmap | Deprecated function(s) in the Seurat package
PCTopCells | Find cells with highest PCA scores
pcTopCells | Deprecated function(s) in the Seurat package
PCTopGenes | Find genes with highest PCA scores
pcTopGenes | Deprecated function(s) in the Seurat package
PlotClusterTree | Plot phylogenetic tree
plotClusterTree | Deprecated function(s) in the Seurat package
PlotNoiseModel | Visualize expression/dropout curve
plotNoiseModel | Deprecated function(s) in the Seurat package
PoissonDETest | Poisson test for UMI-count based data
posterior.plot | Deprecated function(s) in the Seurat package
print.pca | Deprecated function(s) in the Seurat package
PrintPCA | Print the results of a PCA analysis
project.pca | Deprecated function(s) in the Seurat package
project.samples | Deprecated function(s) in the Seurat package
ProjectPCA | Project Principal Components Analysis onto full dataset

## -- R --

Read10X | Load in data from 10X
refined.mapping | Deprecated function(s) in the Seurat package
RefinedMapping | Quantitative refinement of spatial inferences
RegressOut | Regress out technical effects and cell cycle
regulatorScore | Deprecated function(s) in the Seurat package
removePC | Deprecated function(s) in the Seurat package
rename.ident | Deprecated function(s) in the Seurat package
RenameIdent | Rename one identity class to another
reorder.ident | Deprecated function(s) in the Seurat package
ReorderIdent | Reorder identity classes
RunDiffusion | Run t-distributed Stochastic Neighbor Embedding
RunTSNE | Run t-distributed Stochastic Neighbor Embedding
run_diffusion | Deprecated function(s) in the Seurat package
run_tsne | Deprecated function(s) in the Seurat package

## -- S --

SampleUMI | Sample UMI
ScaleData | Scale and center the data
set.all.ident | Deprecated function(s) in the Seurat package
set.ident | Deprecated function(s) in the Seurat package
SetAllIdent | Switch identity class definition to another variable
SetIdent | Set identity class information
Setup | Setup Seurat object
setup | Deprecated function(s) in the Seurat package
seurat | The Seurat Class
seurat-class | The Seurat Class
Seurat-deprecated | Deprecated function(s) in the Seurat package
spatial.de | Deprecated function(s) in the Seurat package
StashIdent | Set identity class information
SubsetCells | Return a subset of the Seurat object
subsetCells | Deprecated function(s) in the Seurat package
SubsetData | Return a subset of the Seurat object
subsetData | Deprecated function(s) in the Seurat package

## -- T --

tnse.plot | Deprecated function(s) in the Seurat package
tobit.test | Deprecated function(s) in the Seurat package
TobitTest | Differential expression testing using Tobit models
tsne.plot | Deprecated function(s) in the Seurat package
TSNEPlot | Plot tSNE map

## -- V --

ValidateClusters | Cluster Validation
ValidateSpecificClusters | Specific Cluster Validation
viz.ica | Deprecated function(s) in the Seurat package
viz.pca | Deprecated function(s) in the Seurat package
VizClassification | Highlight classification results
VizICA | Visualize ICA genes
VizPCA | Visualize PCA genes
VlnPlot | Single cell violin plot
vlnPlot | Deprecated function(s) in the Seurat package

## -- W --

which.cells | Deprecated function(s) in the Seurat package
WhichCells | Identify cells matching certain criteria