All functions

aggregateFeatures

Aggregate Features

aggregateReplicates

Aggregate Replicates

bcbio bcbio<-

bcbioSCDataSet Object Accessors

bcbioSCDataSet-class

bcbioSCDataSet

bcbioSCFiltered-class

bcbioSCFiltered

bcbioSingleCell-package

bcbioSingleCell

calculateMetrics

Calculate Cellular Barcode Metrics Summary

cellCycleMarkers

Cell-Cycle Markers

cellTypeMarkers

Cell-Type Markers

coerce-bcbioSCFiltered-seurat

Coerce bcbioSCFiltered to seurat Object

counts

Counts Accessor

.quantileBreaks

Create Breaks Based on Quantiles of the Data

filterCells

Filter Cells

interestingGroups

Interesting Groups

knownMarkersDetected

Known Markers Detected

loadCellRanger

Load 10X Genomics CellRanger Data

loadSingleCellRun

Load bcbio Single-Cell RNA-Seq Run

metadataTable

Metadata Table

metrics

Sample Barcode Metrics

pcCutoff

Determine PC Cutoff

plotCellCounts

Plot Cell Counts

plotFeatures

Plot Features of a Data Set

plotGenesPerCell

Plot Genes per Cell

plotKnownMarkers

Plot Known Markers

plotMarkers

Plot Gene Markers

plotMitoRatio

Plot Mitochondrial Transcript Abundance

plotNovelty

Plot Novelty Score

plotReadsPerCell

Plot Read Counts per Cell

plotTopMarkers

Plot Top Markers

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

selectSamples

Select Samples

subsetPerSample

Subset Per Sample

topBarcodes

Top Barcodes

topMarkers

Top Markers