API for Seurat
Tools for Single Cell Genomics

Global functions
AUCMarkerTest Source code
AddImputedScore Man page Source code
AddMetaData Man page Source code
AddModuleScore Man page Source code
AddSamples Man page Source code
AddSmoothedScore Man page Source code
AlignSubspace Man page Source code
AllNeighborCells Source code
AssessNodes Man page Source code
AssessSplit Man page Source code
AverageDetectionRate Man page Source code
AverageExpression Man page Source code
AveragePCA Man page Source code
BicorPrep Source code
BiweightMidcor Source code
BlackAndWhite Man page Source code
BlendColors Source code
BlendPlot Source code
BuildClusterTree Man page Source code
BuildRFClassifier Man page Source code
BuildSNN Man page Source code
CalcConnectivity Source code
CalcInfoExists Source code
CalcInsitu Source code
CalcLDProj Source code
CalcProjectedVar Source code
CalcSNNSparse Source code
CalcVarExpRatio Man page Source code
CanonCor Source code
CaseMatch Man page Source code
CellCentroid Source code
CellCycleScoring Man page Source code
CellPlot Man page Source code
CheckGenes Source code
CheckGroup Source code
ClassifyCells Man page Source code
CoefVar Source code
CollapseSpeciesExpressionMatrix Man page Source code
ColorTSNESplit Man page Source code
CountGreaterThan Source code
CreateSeuratObject Man page Source code
CustomDistance Man page Source code
CustomNormalize Source code
CustomPalette Man page Source code
DBClustDimension Man page Source code
DBclust_dimension Man page Source code
DESeq2DETest Man page Source code
DFT Source code
DMEmbed Man page Source code
DMPlot Man page Source code
DarkTheme Man page Source code
DiffExpTest Man page Source code
DiffTTest Man page Source code
DifferentialAUC Source code
DifferentialLRT Source code
DifferentialTobit Source code
DimElbowPlot Man page Source code
DimHeatmap Man page Source code
DimPlot Man page Source code
DimTopCells Man page Source code
DimTopGenes Man page Source code
DoHeatmap Man page Source code
DoKMeans Man page Source code
DotPlot Man page Source code
DotPlotOld Man page Source code
EmpiricalP Source code
ExactCellCentroid Source code
ExpMean Man page Source code
ExpSD Man page Source code
ExpVar Man page Source code
ExtractField Man page Source code
FastCov Source code
FastCovMats Source code
FastExpMean Source code
FastLogVMR Source code
FastMatMult Source code
FastRBind Source code
FastRowScale Source code
FastSparseRowScale Source code
FastWhichCells Man page Source code
FeatureHeatmap Man page Source code
FeatureLocator Man page Source code
FeaturePlot Man page Source code
FetchClosest Source code
FetchData Man page Source code
FillSlot Source code
FillWhiteSpace Source code
FilterCells Man page Source code
FindAllMarkers Man page Source code
FindAllMarkersNode Man page Source code
FindClusters Man page Source code
FindConservedMarkers Man page Source code
FindMarkers Man page Source code
FindMarkersNode Man page Source code
FindVariableGenes Man page Source code
FisherIntegrate Source code
FitGeneK Man page Source code
FitGeneMix Source code
GGpointToBase Source code
GenePlot Man page Source code
GenesInCluster Man page Source code
GetAllCalcParam Source code
GetAllInternalNodes Source code
GetAssayData Man page Source code
GetCalcParam Source code
GetCellEmbeddings Man page Source code
GetCentroids Man page Source code
GetClusters Man page Source code
GetDescendants Source code
GetDimReduction Man page Source code
GetGeneLoadings Man page Source code
GetLeftDescendants Source code
GetRightDescendants Source code
GetTopGenes Source code
GroupSingletons Source code
Hbeta Source code
HeatmapNode Man page Source code Source code
HoverLocator Man page Source code
ICA Man page Source code
ICAEmbed Man page Source code
ICALoad Man page Source code
ICAPlot Man page Source code
ICHeatmap Man page Source code
ICTopCells Man page Source code
ICTopGenes Man page Source code
InitialMapping Man page Source code
JackRandom Source code
JackStraw Man page Source code
JackStrawPlot Man page Source code
JoyPlot Man page Source code
KClustDimension Man page Source code
KMeansHeatmap Man page Source code
Kclust_dimension Man page Source code
KullbackFun Source code
LengthCheck Source code
LogAdd Source code
LogNorm Source code
LogNormalize Man page Source code
LogVMR Man page Source code
MASTDETest Man page Source code
MakeSparse Man page Source code
MapCell Source code
MapVals Source code
MarkerTest Man page Source code
MatrixRowShuffle Man page Source code
MeanGreaterThan Source code
MeanVarPlot Man page Source code Source code
MergeNode Man page Source code
MergeSeurat Man page Source code
MinMax Man page Source code
NBModelComparison Source code
NBResiduals Source code
NegBinomDETest Man page Source code
NegBinomRegDETest Man page Source code
NeighborCells Source code
NoGrid Source code
NodeHasChild Source code
NodeHasOnlyChildren Source code
NodeHeatmap Source code
NormalizeData Man page Source code
NumberClusters Man page Source code
OldDoHeatmap Man page Source code
PCA Man page Source code
PCAEmbed Man page Source code
PCAFast Source code Source code
PCALoad Man page Source code
PCAPlot Man page Source code
PCASigGenes Man page Source code
PCElbowPlot Man page Source code
PCHeatmap Man page Source code
PCTopCells Man page Source code
PCTopGenes Man page Source code
PercentAbove Source code
PlotBuild Source code
PlotClusterTree Man page Source code
PlotDim Source code
PointLocator Source code
PoissonDETest Man page Source code
PosteriorPlot Source code
PrepDR Source code
PrintAlignSubspaceParams Man page Source code
PrintCCAParams Man page Source code
PrintCalcParams Man page Source code
PrintCalcVarExpRatioParams Man page Source code
PrintDMParams Man page Source code
PrintDim Man page Source code
PrintFindClustersParams Man page Source code
PrintICA Man page Source code
PrintICAParams Man page Source code
PrintPCA Man page Source code
PrintPCAParams Man page Source code
PrintSNNParams Man page Source code
PrintTSNEParams Man page Source code
ProjectDim Man page Source code
ProjectPCA Man page Source code
PurpleAndYellow Man page Source code
Read10X Man page Source code
ReferenceRange Source code
RefinedMapping Man page Source code
RegressOut Man page Source code
RegressOutNB Source code
RegressOutNBreg Source code
RegressOutResid Source code
RegularizedTheta Source code
RemoveCalcParams Source code
RemoveFromTable Man page Source code
RenameIdent Man page Source code
ReorderIdent Man page Source code
ResetPar Source code
RowMergeMatrices Source code
RowMergeSparseMatrices Source code
RunCCA Man page Source code
RunClassifier Source code
RunDiffusion Man page Source code
RunICA Man page Source code
RunModularityClustering Source code
RunPCA Man page Source code
RunTSNE Man page Source code
RunUMISampling Source code
RunUMISamplingPerCell Source code
Same Source code
SampleUMI Man page Source code
SaveClusters Man page Source code
ScaleData Man page Source code
ScaleDataR Man page Source code
SetAllIdent Man page Source code
SetAssayData Man page Source code
SetCalcParams Source code
SetClusters Man page Source code
SetDimReduction Man page Source code
SetIdent Man page Source code
SetIfNull Source code
SetLegendPointsGG Source code
SetLegendTextGG Source code
SetQuantile Source code
SetSingleCalcParam Source code
SetXAxisGG Source code
SetYAxisGG Source code
Seurat-deprecated Man page
ShiftCell Source code
Shuffle Man page Source code
SingleFeaturePlot Source code
SingleJoyPlot Source code
SingleVlnPlot Source code
SplitDotPlotGG Man page Source code
Standardize Source code
StashIdent Man page Source code
SubsetColumn Man page Source code
SubsetData Man page Source code
SubsetRow Man page Source code
TSNEPlot Man page Source code
TobitDiffExpTest Source code
TobitFitter Source code
TobitTest Man page Source code
UpdateSeuratObject Man page Source code
ValidateClusters Man page Source code
ValidateSpecificClusters Man page Source code
VariableGenePlot Man page Source code
VarianceGreaterThan Source code
VizClassification Man page Source code
VizDimReduction Man page Source code
VizICA Man page Source code
VizPCA Man page Source code
VlnPlot Man page Source code
WeightedEuclideanDistance Source code
WhichCells Man page Source code
WilcoxDETest Man page Source code
XCellCentroid Source code
YCellCentroid Source code
addImputedScore Man page Source code
addMetaData Man page Source code
addSmoothedScore Man page Source code
add_samples Man page Source code
average.expression Man page Source code
average.pca Man page Source code
batch.gene Man page Source code
bimodLikData Source code
buildClusterTree Man page Source code
calc.insitu Man page Source code
calcNoiseModels Man page Source code
calinskiPlot Man page Source code
cc.genes Man page
cell.cor.matrix Man page Source code
cellPlot Man page Source code
cluster.alpha Man page Source code
d2p_cell Source code
diffExp.test Man page Source code
doHeatMap Man page Source code
doKMeans Man page Source code
dot.plot Man page Source code
feature.heatmap Man page Source code
feature.plot Man page Source code
feature.plot.keynote Man page Source code
fetch.data Man page Source code
find.markers Man page Source code
find.markers.node Man page Source code
find_all_markers Man page Source code
fit.gene.k Man page Source code
fit.gene.mix Man page Source code
gene.cor.matrix Man page Source code
genePlot Man page Source code
geneScorePlot Man page Source code
genes.in.cluster Man page Source code
get.centroids Man page Source code
getNewScore Man page Source code
heatmap2NoKey Source code
icHeatmap Man page Source code
icTopGenes Man page Source code
ica Man page Source code
ica.plot Man page Source code
initial.mapping Man page Source code
iter.k.fit Source code
jackRandom Man page Source code Source code
jackStraw Man page Source code
jackStraw.permutation.test Man page Source code
jackStrawFull Man page Source code
jackStrawMC Man page Source code
jackStrawPlot Man page Source code
kMeansHeatmap Man page Source code
lasso.fxn Source code
map.cell Man page Source code
map.cell.score Source code
marker.test Man page Source code
minusc Man page Source code Source code
minusr Man page Source code Source code
myPalette Source code Source code
pbmc_small Man page
pcHeatmap Man page Source code
pcTopCells Man page Source code
pcTopGenes Man page Source code
pca Man page Source code
pca.plot Man page Source code
pca.sig.genes Man page Source code
plotClusterTree Man page Source code
plotNoiseModel Man page Source code
posterior.plot Man page Source code
project.pca Man page Source code
project.samples Man page Source code
project_map Source code
refined.mapping Man page Source code
regulatorScore Man page Source code
removePC Man page Source code
rename.ident Man page Source code
run_diffusion Man page Source code
run_tsne Man page Source code
set.all.ident Man page Source code
set.ident Man page Source code
seurat Man page
seurat-class Man page
show Man page
show,seurat-method Man page
slimdmvnorm Source code
spatial.de Man page Source code
subsetCells Man page Source code
subsetData Man page Source code
tnse.plot Man page
tobit.test Man page Source code
tsne.plot Man page Source code
viz.ica Man page Source code
viz.pca Man page Source code
vlnPlot Man page Source code
which.cells Man page Source code
writ.table Man page Source code Source code
Seurat documentation built on Nov. 17, 2017, 7:10 a.m.