S4 classes

CellCycleMarkers()

Cell-cycle markers

CellTypeMarkers()

Cell-type markers

KnownMarkers()

Known markers

SeuratMarkers()

Seurat markers

SeuratMarkersPerCluster()

Seurat markers per cluster

coerce

Force an object to belong to a class

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

Show an object

summary()

Object summaries

Differential expression

diffExp()

Differential expression

diffExpPerCluster()

Differential expression per cluster

findMarkers()

Find cluster-specific marker genes

Cluster statistics

cellCountsPerCluster()

Cell counts per cluster

cellTypesPerCluster()

Cell types per cluster

clusterCellCountsPerSample()

Cluster cell counts per sample

Marker analysis

clusterID()

Cluster identifier

knownMarkers() knownMarkersDetected() plotKnownMarkersDetected() readCellTypeMarkers() sanitizeMarkers() importCellCycleMarkersFromGoogle() importCellTypeMarkersFromGoogle() runZinbwave()

Defunct functions

topMarkers()

Top markers

Plots

plotCellCountsPerCluster()

Plot cell counts per cluster

plotCellTypesPerCluster()

Plot cell types per cluster

plotCounts() plotDot() 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

plotTopMarkers()

Plot top markers

Cell markers

cell_cycle_markers

Cell-cycle markers

cell_type_markers

Cell-type markers

Example data

seurat

Seurat example

seurat_all_markers

Seurat all markers example

seurat_known_markers

Seurat known markers example