S4 classes

CellCycleMarkers-class

Cell-cycle markers

CellCycleMarkers()

Cell-cycle markers

CellTypeMarkers-class

Cell-type markers

CellTypeMarkers()

Cell-type markers

KnownMarkers-class

Known markers

KnownMarkers()

Known markers

SeuratMarkers-class

Seurat markers

SeuratMarkers() SeuratMarkersPerCluster()

Seurat markers

SeuratMarkersPerCluster-class

Seurat markers per cluster

as

Force an object to belong to a class

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

Show an object

summary(<SeuratMarkers>) summary(<SeuratMarkersPerCluster>)

Object summaries

Differential expression

diffExp(<SingleCellExperiment>) diffExp(<seurat>)

Differential expression

diffExpPerCluster(<SingleCellExperiment>) diffExpPerCluster(<seurat>)

Differential expression per cluster

findMarkers(<SingleCellExperiment>) findMarkers(<seurat>)

Find cluster-specific marker genes

runZinbwave()

Perform dimensionality reduction using a ZINB regression model with gene and cell-level covariates.

Cluster statistics

cellCountsPerCluster(<SingleCellExperiment>) cellCountsPerCluster(<seurat>)

Cell counts per cluster

cellTypesPerCluster(<KnownMarkers>)

Cell types per cluster

clusterCellCountsPerSample(<SingleCellExperiment>) clusterCellCountsPerSample(<seurat>)

Cluster cell counts per sample

Marker analysis

clusterID(<SingleCellExperiment>) clusterID(<seurat>)

Cluster identifier

importCellCycleMarkersFromGoogle() importCellTypeMarkersFromGoogle()

Import markers from Google Sheets

knownMarkers() knownMarkersDetected() plotKnownMarkersDetected() readCellTypeMarkers() sanitizeMarkers()

Defunct functions

topMarkers(<SeuratMarkersPerCluster>)

Top markers

Plots

plotCellTypesPerCluster(<SingleCellExperiment>) plotCellTypesPerCluster(<seurat>)

Plot cell types per cluster

plotFeature(<SingleCellExperiment>) plotFeature(<seurat>)

Plot feature

plotGene(<SingleCellExperiment>) plotGene(<seurat>) plotDot(<SingleCellExperiment>) plotDot(<seurat>) plotViolin(<SingleCellExperiment>) plotViolin(<seurat>)

Plot gene expression

plotKnownMarkers(<SingleCellExperiment>,<KnownMarkers>) plotKnownMarkers(<seurat>,<KnownMarkers>)

Plot known markers

plotMarker(<SingleCellExperiment>) plotMarker(<seurat>)

Plot cell-type-specific gene markers

plotPCElbow(<seurat>)

Plot principal component elbow

plotReducedDim(<SingleCellExperiment>) plotReducedDim(<seurat>) plotTSNE(<SingleCellExperiment>) plotTSNE(<seurat>) plotUMAP(<SingleCellExperiment>) plotUMAP(<seurat>) plotPCA(<SingleCellExperiment>) plotPCA(<seurat>)

Plot reduced dimensions

plotTopMarkers(<SingleCellExperiment>) plotTopMarkers(<seurat>)

Plot top markers

Cell markers

cell_cycle_markers

Cell-cycle markers

cell_type_markers

Cell-type markers

Example data

all_markers_small

Sanitized markers example

known_markers_small

Known markers example

seurat_small

Seurat example