Man pages for nukappa/seurat_v2
Seurat : R toolkit for single cell genomics

AddImputedScoreCalculate imputed expression values
AddMetaDataAdd Metadata
AddSamplesAdd samples into existing Seurat object.
AddSmoothedScoreCalculate smoothed expression values
AssessNodesAssess Internal Nodes
AssessSplitAssess Cluster Split
AverageExpressionAveraged gene expression by identity class
AveragePCAAverage PCA scores by identity class
BatchGeneIdentify potential genes associated with batch effects
BuildClusterTreePhylogenetic Analysis of Identity Classes
BuildRFClassifierBuild Random Forest Classifier
BuildSNNSNN Graph Construction
CellPlotCell-cell scatter plot
ClassifyCellsClassify New Data
ClusterAlphaProbability of detection by identity class
ColorTSNESplitColor tSNE Plot Based on Split
DBClustDimensionPerform spectral density clustering on single cells
DiffExpTestLikelihood ratio test for zero-inflated data
DiffTTestDifferential expression testing using Student's t-test
DimPlotDimensional reduction plot
DoHeatmapGene expression heatmap
DoKMeansK-Means Clustering
DotPlotDot plot visualization
FeatureHeatmapVizualization of multiple features
FeaturePlotVisualize 'features' on a dimensional reduction plot
FetchDataAccess cellular data
FindAllMarkersGene expression markers for all identity classes
FindAllMarkersNodeFind all markers for a node
FindClustersCluster Determination
FindMarkersGene expression markers of identity classes
FindMarkersNodeGene expression markers of identity classes defined by a...
FitGeneKBuild mixture models of gene expression
GenePlotScatter plot of single cell data
GetCentroidsGet cell centroids
HeatmapNodeNode Heatmap
ICARun Independent Component Analysis on gene expression
ICAPlotPlot ICA map
ICHeatmapIndependent component heatmap
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
LogNormalizeNormalize raw data
MakeSparseMake object sparse
MarkerTestROC-based marker discovery
MeanVarPlotIdentify variable genes
MergeNodeMerge subchilden of a node
MergeSeuratMerge Seurat Objects
NegBinomDETestNegative binomial test for UMI-count based data
PCARun Principal Component Analysis on gene expression
PCAFastRun Principal Component Analysis on gene expression using...
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
PlotNoiseModelVisualize expression/dropout curve
PoissonDETestPoisson test for UMI-count based data
PrintPCAPrint the results of a PCA analysis
ProjectPCAProject Principal Components Analysis onto full dataset
Read10XLoad in data from 10X
RefinedMappingQuantitative refinement of spatial inferences
RegressOutRegress out technical effects and cell cycle
RenameIdentRename one identity class to another
ReorderIdentReorder identity classes
RunDiffusionRun t-distributed Stochastic Neighbor Embedding
RunTSNERun t-distributed Stochastic Neighbor Embedding
SampleUMISample UMI
ScaleDataScale and center the data
SetAllIdentSwitch identity class definition to another variable
SetIdentSet identity class information
SetupSetup Seurat object
seuratThe Seurat Class
Seurat-deprecatedDeprecated function(s) in the Seurat package
StashIdentSet identity class information
SubsetCellsReturn a subset of the Seurat object
SubsetDataReturn a subset of the Seurat object
TobitTestDifferential expression testing using Tobit models
TSNEPlotPlot tSNE map
ValidateClustersCluster Validation
ValidateSpecificClustersSpecific Cluster Validation
VizClassificationHighlight classification results
VizICAVisualize ICA genes
VizPCAVisualize PCA genes
VlnPlotSingle cell violin plot
WhichCellsIdentify cells matching certain criteria
nukappa/seurat_v2 documentation built on May 23, 2017, 5:26 p.m.