All functions

aggregateFeatures

Aggregate Features

aggregateReplicates

Aggregate Replicates

annotable

Ensembl Annotations

bcbio bcbio<-

bcbioSingleCell Additional bcbio Run Data Accessor

bcbioSingleCell-class

bcbioSingleCell

bcbioSingleCell-package

bcbioSingleCell

calculateMetrics

Calculate Cellular Barcode Metrics Summary

cell2sample

Cell to Sample Mappings

cellCycleMarkers

Cell-Cycle Markers

cellTypeMarkers

Cell-Type Markers

cellTypesPerCluster

Cell Types per Cluster

coerce

Coerce Object

counts

Counts Accessor

fetchPCAData

Fetch PCA Dimensions and Cellular Metadata

fetchTSNEData

Fetch t-SNE Locations and Cellular Metadata

fetchTSNEExpressionData

Fetch t-SNE Locations, Cellular Metadata and Expression of Genes

filterCells

Filter Cells

flatFiles

Get Flat Files from S4 Object

interestingGroups interestingGroups<-

Interesting Groups

knownMarkersDetected

Known Markers Detected

loadCellRanger

Load 10X Genomics CellRanger Data

loadSingleCell

Load bcbio Single-Cell RNA-Seq Data

metrics

Sample Barcode Metrics

pcCutoff

Determine PC Cutoff

plotCellCounts

Plot Cell Counts

plotCellTypesPerCluster

Plot Cell Types per Cluster

plotDot

Plot Dot

plotFeatures

Plot Features

plotGenesPerCell

Plot Genes per Cell

plotKnownMarkers

Plot Known Markers

plotMarkers

Plot Cell-Type Gene Markers

plotMarkerTSNE

Plot Marker t-SNE

plotMitoRatio

Plot Mitochondrial Transcript Abundance

plotMitoVsCoding

Plot Mitochondrial Counts vs. Coding Counts

plotNovelty

Plot Novelty Score

plotPCA

Plot Principal Component Analysis (PCA)

plotQC

Quality Control Plots

plotReadsPerCell

Plot Read Counts per Cell

plotTopMarkers

Plot Top Markers

plotTSNE

Plot t-SNE

plotUMIsPerCell

Plot UMIs per Cell

plotUMIsVsGenes

Plot UMI and Gene Correlation

plotZerosVsDepth

Plot Percentage of Zeros vs. Library Depth

prepareSingleCellTemplate

Prepare Single-Cell RNA-Seq RMarkdown Template

quantileHeatmap

Heatmap with Quantile Breaks

readMarkers

Read Known Markers

sampleMetadata

Sample Metadata

sanitizeMarkers

Sanitize Markers Output

selectSamples

Select Samples

subsetPerSample

Subset Per Sample

topBarcodes

Top Barcodes

topMarkers

Top Markers