S4 Object

bcbioSingleCell-package

bcbioSingleCell

bcbioSingleCell()

bcbioSingleCell Object and Constructor

coerce

Methods for Coercing an Object to a Class

show(<bcbioSingleCell>)

Show an Object

`[`(<bcbioSingleCell>,<ANY>,<ANY>,<ANY>)

Subset Object

updateObject(<bcbioSingleCell>)

Update Object

Read Functions

readCellRanger()

Read 10X Genomics Cell Ranger Data

readCellTypeMarkers()

Read Cell Type Markers File

Data Functions

aggregateReplicates(<bcbioSingleCell>)

Aggregate Replicates

cell2sample()

Cell to Sample Mappings

fetchGeneData() fetchPCAData() fetchTSNEData() fetchTSNEExpressionData() fetchUMAPData() fetchUMAPExpressionData()

Fetch Data Functions

mapCellsToSamples()

Define Cell to Sample Mappings

selectSamples(<SingleCellExperiment>)

Select Samples

sampleData(<SingleCellExperiment>) sampleData(<seurat>) `sampleData<-`(<SingleCellExperiment>,<DataFrame>) `sampleData<-`(<seurat>,<DataFrame>)

Sample Data

subsetPerSample()

Subset Per Sample

topBarcodes()

Top Barcodes

Quality Control Functions

metrics(<matrix>) metrics(<dgCMatrix>) metrics(<dgTMatrix>) metrics(<SingleCellExperiment>) metrics(<seurat>)

Sample Barcode Metrics

metricsPerSample()

Metrics per Sample

filterCells()

Filter Cells

plotQC(<SingleCellExperiment>) plotQC(<seurat>)

Quality Control Plots

plotCellCounts()

Plot Cell Counts

plotReadsPerCell()

Plot Read Counts per Cell

plotUMIsPerCell()

Plot UMIs per Cell

plotGenesPerCell()

Plot Genes per Cell

plotUMIsVsGenes()

Plot UMI and Gene Correlation

plotNovelty()

Plot Novelty Score

plotMitoRatio()

Plot Mitochondrial Transcript Abundance

plotMitoVsCoding()

Plot Mitochondrial vs. Coding Counts

plotZerosVsDepth()

Plot Percentage of Zeros vs. Library Depth

barcodeRanksPerSample()

Barcode Ranks per Sample

plotBarcodeRanks()

Plot Barcode Ranks

plotFeatureTSNE() plotFeatureUMAP()

Plot Feature

Clustering Functions

cellTypesPerCluster()

Cell Types per Cluster

plotCellTypesPerCluster()

Plot Cell Types per Cluster

plotPCElbow()

Plot PC Elbow

fetchGeneData() fetchPCAData() fetchTSNEData() fetchTSNEExpressionData() fetchUMAPData() fetchUMAPExpressionData()

Fetch Data Functions

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

Plot Dimensional Reduction

plotFeatureTSNE() plotFeatureUMAP()

Plot Feature

plotKnownMarkersDetected() plotMarkerTSNE() plotMarkerUMAP() plotTopMarkers()

Plot Cell-Type-Specific Gene Markers

Gene Expression Functions

plotGene(<seurat>)

Plot Gene

plotDot(<seurat>)

Plot Dot

plotKnownMarkersDetected() plotMarkerTSNE() plotMarkerUMAP() plotTopMarkers()

Plot Cell-Type-Specific Gene Markers

plotViolin(<seurat>)

Plot Violin

Differential Expression Functions

diffExp()

Differential Expression

knownMarkersDetected()

Known Markers Detected

sanitizeMarkers()

Sanitize Markers Output

topMarkers()

Top Markers

Plot Functions

plotBarcodeRanks()

Plot Barcode Ranks

plotCellCounts()

Plot Cell Counts

plotCellTypesPerCluster()

Plot Cell Types per Cluster

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

Plot Dimensional Reduction

plotDot(<seurat>)

Plot Dot

plotFeatureTSNE() plotFeatureUMAP()

Plot Feature

plotGene(<seurat>)

Plot Gene

plotGenesPerCell()

Plot Genes per Cell

plotKnownMarkersDetected() plotMarkerTSNE() plotMarkerUMAP() plotTopMarkers()

Plot Cell-Type-Specific Gene Markers

plotMitoRatio()

Plot Mitochondrial Transcript Abundance

plotMitoVsCoding()

Plot Mitochondrial vs. Coding Counts

plotNovelty()

Plot Novelty Score

plotPCElbow()

Plot PC Elbow

plotQC(<SingleCellExperiment>) plotQC(<seurat>)

Quality Control Plots

plotReadsPerCell()

Plot Read Counts per Cell

plotUMIsPerCell()

Plot UMIs per Cell

plotUMIsVsGenes()

Plot UMI and Gene Correlation

plotViolin(<seurat>)

Plot Violin

plotZerosVsDepth()

Plot Percentage of Zeros vs. Library Depth

R Markdown Functions

prepareSingleCellTemplate()

Prepare Single-Cell RNA-Seq R Markdown Template

Internal Data

cellCycleMarkers

Cell-Cycle Markers

cellTypeMarkers

Cell-Type Markers

Example Data

all_markers_small

Sanitized Markers Example

cellranger_small

Cell Ranger Example

indrops_small

inDrops Example

known_markers_small

Known Markers Example

seurat_small

Seurat Example