S4 classes

CellCycleMarkers-class

Cell-cycle markers

CellTypeMarkers-class

Cell-type markers

KnownMarkers-class

Known markers

SeuratMarkers-class

Seurat markers

SeuratMarkersPerCluster-class

Seurat markers per cluster

CellCycleMarkers() importCellCycleMarkers()

Cell-cycle markers

CellTypeMarkers() importCellTypeMarkers()

Cell-type markers

KnownMarkers()

Known markers

SeuratMarkers() SeuratMarkersPerCluster()

Sanitize Seurat markers

findMarkers()

Find cluster-specific marker genes

plotKnownMarkers()

Plot known markers

plotTopMarkers()

Plot top markers

seuratAllMarkers

Seurat all markers example

seuratKnownMarkers

Seurat known markers example

topMarkers()

Top markers

coerce

Force an object to belong to a class

show(<CellCycleMarkers>) show(<CellTypeMarkers>)

Show an object

summary()

Object Summaries

Counts

cpm()

Counts per million

Clustering

cellCountsPerCluster()

Cell counts per cluster

cellTypesPerCluster()

Cell types per cluster

clusters()

Cluster identifiers

normalize()

Normalize expression using pre-computed size factors

Differential expression

SeuratMarkers() SeuratMarkersPerCluster()

Sanitize Seurat markers

diffExp()

Differential expression

diffExpPerCluster()

Differential expression per cluster

findMarkers()

Find cluster-specific marker genes

topMarkers()

Top markers

Plots

plotCellCountsPerCluster()

Plot cell counts per cluster

plotCellTypesPerCluster()

Plot cell types per cluster

plotCounts() plotDots() plotViolin()

Plot counts

plotFeature()

Plot feature

plotKnownMarkers()

Plot known markers

plotMarker()

Plot cell-type-specific gene markers

plotPCElbow()

Plot principal component elbow

plotReducedDim() plotPCA() plotTSNE() plotUMAP()

Plot reduced dimensions

plotStackedBarPlot()

Plot stacked bar plot

plotTopMarkers()

Plot top markers

Wrappers

runSeurat()

Run Seurat

runZinbwave()

Run ZINB-WaVE

Data