# Tools for Single Cell Genomics

## Documentation for package ‘Seurat’ version 2.2.1

- DESCRIPTION file.

## Help Pages

A B C D E F G H I J K L M N O P R S T U 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
AddModuleScore | Calculate module scores for gene expression programs in single cells
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
AlignSubspace | Align subspaces using dynamic time warping (DTW)
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
AverageDetectionRate | Probability of detection by identity class
AverageExpression | Averaged gene expression by identity class
AveragePCA | Average PCA scores by identity class

## -- B --

batch.gene | Deprecated function(s) in the Seurat package
BlackAndWhite | A black and white color palette
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
CalcAlignmentMetric | Calculate an alignment score
calcNoiseModels | Deprecated function(s) in the Seurat package
CalcVarExpRatio | Calculate the ratio of variance explained by ICA or PCA to CCA
calinskiPlot | Deprecated function(s) in the Seurat package
CaseMatch | Match the case of character vectors
cc.genes | Cell cycle genes
cell.cor.matrix | Deprecated function(s) in the Seurat package
CellCycleScoring | Score cell cycle phases
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
CollapseSpeciesExpressionMatrix | Slim down a multi-species expression matrix, when only one species is primarily of interenst.
ColorTSNESplit | Color tSNE Plot Based on Split
CreateSeuratObject | Initialize and setup the Seurat object
CustomDistance | Run a custom distance function on an input data matrix
CustomPalette | Create a custom color palette

## -- D --

DarkTheme | Dark Theme
DBClustDimension | Perform spectral density clustering on single cells
DBclust_dimension | Deprecated function(s) in the Seurat package
DESeq2DETest | Differential expression using DESeq2
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
DimElbowPlot | Quickly Pick Relevant Dimensions
DimHeatmap | Dimensional reduction heatmap
DimPlot | Dimensional reduction plot
DimTopCells | Find cells with highest scores for a given dimensional reduction technique
DimTopGenes | Find genes with highest scores for a given dimensional reduction technique
DMEmbed | Diffusion Maps Cell Embeddings Accessor Function
DMPlot | Plot Diffusion map
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
DotPlotOld | Old Dot plot visualization (pre-ggplot implementation) Intuitive way of visualizing how gene expression changes across different identity classes (clusters). The size of the dot encodes the percentage of cells within a class, while the color encodes the AverageExpression level of 'expressing' cells (green is high).

## -- E --

ExpMean | Calculate the mean of logged values
ExpSD | Calculate the standard deviation of logged values
ExpVar | Calculate the variance of logged values
ExtractField | Extract delimiter information from a string.

## -- F --

FastWhichCells | FastWhichCells Identify cells matching certain criteria (limited to character values)
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
FeatureLocator | Feature Locator
FeaturePlot | Visualize 'features' on a dimensional reduction plot
fetch.data | Deprecated function(s) in the Seurat package
FetchData | Access cellular data
FilterCells | Return a subset of the Seurat object
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
FindConservedMarkers | Finds markers that are conserved between the two groups
FindMarkers | Gene expression markers of identity classes
FindMarkersNode | Gene expression markers of identity classes defined by a phylogenetic clade
FindVariableGenes | Identify variable genes
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
GenesInCluster | GenesInCluster
get.centroids | Deprecated function(s) in the Seurat package
GetAssayData | Accessor function for multimodal data
GetCellEmbeddings | Dimensional Reduction Cell Embeddings Accessor Function
GetCentroids | Get cell centroids
GetClusters | Get Cluster Assignments
GetDimReduction | Dimensional Reduction Accessor Function
GetGeneLoadings | Dimensional Reduction Gene Loadings Accessor Function
getNewScore | Deprecated function(s) in the Seurat package

## -- H --

HeatmapNode | Deprecated function(s) in the Seurat package
HoverLocator | Hover Locator

## -- I --

ICA | Deprecated function(s) in the Seurat package
ica | Deprecated function(s) in the Seurat package
ica.plot | Deprecated function(s) in the Seurat package
ICAEmbed | ICA Cell Embeddings Accessor Function
ICALoad | ICA Gene Loadings Accessor Function
ICAPlot | Plot ICA map
ICHeatmap | Independent component heatmap
icHeatmap | Deprecated function(s) in the Seurat package
ICTopCells | Find cells with highest ICA scores
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 --

jackRandom | Deprecated function(s) in the Seurat package
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
JoyPlot | 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 | Plot k-means clusters
kMeansHeatmap | Deprecated function(s) in the Seurat package

## -- L --

LogNormalize | Normalize raw data
LogVMR | Calculate the variance to mean ratio of logged values

## -- 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
MASTDETest | Differential expression using MAST
MatrixRowShuffle | Independently shuffle values within each row of a matrix
MeanVarPlot | Deprecated function(s) in the Seurat package
MergeNode | Merge childen of a node
MergeSeurat | Merge Seurat Objects
MetageneBicorPlot | Plot CC bicor saturation plot
MinMax | Apply a ceiling and floor to all values in a matrix
minusc | Deprecated function(s) in the Seurat package
minusr | Deprecated function(s) in the Seurat package

## -- N --

NegBinomDETest | Negative binomial test for UMI-count based data
NegBinomRegDETest | Negative binomial test for UMI-count based data (regularized version)
NormalizeData | Normalize Assay Data
NumberClusters | Convert the cluster labels to a numeric representation

## -- O --

OldDoHeatmap | Gene expression heatmap

## -- P --

pbmc_small | A small example version of the PBMC dataset
PCA | Deprecated function(s) in the Seurat package
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
PCAEmbed | PCA Cell Embeddings Accessor Function
PCALoad | PCA Gene Loadings Accessor Function
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 | Deprecated function(s) in the Seurat package
PoissonDETest | Poisson test for UMI-count based data
posterior.plot | Deprecated function(s) in the Seurat package
PrintAlignSubspaceParams | Print AlignSubspace Calculation Parameters
PrintCalcParams | Print the calculation
PrintCalcVarExpRatioParams | Print Parameters Associated with CalcVarExpRatio
PrintCCAParams | Print CCA Calculation Parameters
PrintDim | Print the results of a dimensional reduction analysis
PrintDMParams | Print Diffusion Map Calculation Parameters
PrintFindClustersParams | Print FindClusters Calculation Parameters
PrintICA | Print the results of a ICA analysis
PrintICAParams | Print ICA Calculation Parameters
PrintPCA | Print the results of a PCA analysis
PrintPCAParams | Print PCA Calculation Parameters
PrintSNNParams | Print SNN Construction Calculation Parameters
PrintTSNEParams | Print TSNE Calculation Parameters
project.pca | Deprecated function(s) in the Seurat package
project.samples | Deprecated function(s) in the Seurat package
ProjectDim | Project Dimensional reduction onto full dataset
ProjectPCA | Project Principal Components Analysis onto full dataset
PurpleAndYellow | A purple and yellow color palette

## -- R --

Read10X | Load in data from 10X
refined.mapping | Deprecated function(s) in the Seurat package
RefinedMapping | Quantitative refinement of spatial inferences
RegressOut | Deprecated function(s) in the Seurat package
regulatorScore | Deprecated function(s) in the Seurat package
RemoveFromTable | Remove data from a table
removePC | Deprecated function(s) in the Seurat package
rename.ident | Deprecated function(s) in the Seurat package
RenameIdent | Rename one identity class to another
ReorderIdent | Reorder identity classes
RidgePlot | Single cell ridge plot
RunCCA | Perform Canonical Correlation Analysis
RunDiffusion | Run diffusion map
RunICA | Run Independent Component Analysis on gene expression
RunMultiCCA | Perform Canonical Correlation Analysis with more than two groups
RunPCA | Run Principal Component Analysis on gene expression using IRLBA
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
SaveClusters | Save cluster assignments to a TSV file
ScaleData | Scale and center the data.
ScaleDataR | Old R based implementation of ScaleData. Scales and centers 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
SetAssayData | Assay Data Mutator Function
SetClusters | Set Cluster Assignments
SetDimReduction | Dimensional Reduction Mutator Function
SetIdent | Set identity class information
seurat | The Seurat Class
seurat-class | The Seurat Class
Seurat-deprecated | Deprecated function(s) in the Seurat package
show | show method for seurat
show-method | show method for seurat
Shuffle | Shuffle a vector
spatial.de | Deprecated function(s) in the Seurat package
SplitDotPlotGG | Split Dot plot visualization
StashIdent | Set identity class information
subsetCells | Deprecated function(s) in the Seurat package
SubsetColumn | Return a subset of columns for a matrix or data frame
SubsetData | Return a subset of the Seurat object
subsetData | Deprecated function(s) in the Seurat package
SubsetRow | Return a subset of rows for a matrix or data frame

## -- 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

## -- U --

UpdateSeuratObject | Update old Seurat object to accomodate new features

## -- V --

ValidateClusters | Cluster Validation
ValidateSpecificClusters | Specific Cluster Validation
VariableGenePlot | View variable genes
viz.ica | Deprecated function(s) in the Seurat package
viz.pca | Deprecated function(s) in the Seurat package
VizClassification | Deprecated function(s) in the Seurat package
VizDimReduction | Visualize Dimensional Reduction genes
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
WilcoxDETest | Differential expression using Wilcoxon Rank Sum
writ.table | Deprecated function(s) in the Seurat package