Man pages for paodan/studySeu
Seurat : R toolkit for single cell genomics

addImputedScoreCalculate imputed expression values
addMetaDataAdd Metadata
addSmoothedScoreCalculate smoothed expression values
average.expressionAveraged gene expression by identity class
average.pcaAverage PCA scores by identity class
batch.geneIdentify potential genes associated with batch effects
buildClusterTreePhylogenetic Analysis of Identity Classes
BuildSNNSNN Graph Construction
cellPlotCell-cell scatter plot
cluster.alphaProbability of detection by identity class
DBclust_dimensionPerform spectral density clustering on single cells
diffExp.testLikelihood ratio test for zero-inflated data
diff.t.testDifferential expression testing using Student's t-test
dim.plotDimensional reduction plot
doHeatMapGene expression heatmap
doKMeansK-Means Clustering
dot.plotDot plot visualization
feature.heatmapVizualization of multiple features
feature.plotVisualize 'features' on a dimensional reduction plot
fetch.dataAccess cellular data
find_all_markersGene expression markers for all identity classes
FindClustersCluster Determination
find.markersGene expression markers of identity classes
find.markers.nodeGene expression markers of identity classes defined by a...
fit.gene.kBuild mixture models of gene expression
genePlotScatter plot of single cell data
get.centroidsGet cell centroids
icaRun Independent Component Analysis on gene expression
ica.plotPlot ICA map
icHeatmapIndependent component heatmap
icTopGenesFind genes with highest ICA scores
initial.mappingInfer spatial origins for single cells
jackStrawDetermine statistical significance of PCA scores.
jackStrawPlotJackStraw Plot
Kclust_dimensionPerform spectral k-means clustering on single cells
marker.testROC-based marker discovery
mean.var.plotIdentify variable genes
pcaRun Principal Component Analysis on gene expression
pca.plotPlot PCA map
pca.sig.genesSignificant genes from a PCA
pcHeatmapPrincipal component heatmap
pcTopCellsFind cells with highest PCA scores
pcTopGenesFind genes with highest PCA scores
plotClusterTreePlot phylogenetic tree
plotNoiseModelVisualize expression/dropout curve
print.pcaPrint the results of a PCA analysis
project.pcaProject Principal Components Analysis onto full dataset
refined.mappingQuantitative refinement of spatial inferences
RegressOutRegress out technical effects and cell cycle
rename.identRename one identity class to another
reorder.identReorder identity classes
run_diffusionRun t-distributed Stochastic Neighbor Embedding
run_tsneRun t-distributed Stochastic Neighbor Embedding
ScaleDataScale and center the data
set.all.identSwitch identity class definition to another variable
set.identSet identity class information
setupSetup Seurat object
seuratThe Seurat Class
subsetCellsReturn a subset of the Seurat object
subsetDataReturn a subset of the Seurat object
tobit.testDifferential expression testing using Tobit models
tsne.plotPlot tSNE map
ValidateClustersCluster Validation
ValidateSpecificClustersSpecific Cluster Validation
viz.icaVisualize ICA genes
viz.pcaVisualize PCA genes
vlnPlotSingle cell violin plot
which.cellsIdentify matching cells
paodan/studySeu documentation built on Jan. 15, 2018, 12:50 a.m.