Package Information

bcbioSingleCell-package

bcbioSingleCell

S4 Object

bcbioSingleCell()

bcbioSingleCell Object and Constructor

combine(<SingleCellExperiment>,<SingleCellExperiment>)

Combine Multiple SingleCellExperiment Objects

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

Extract or Replace Parts of an Object

show(<bcbioSingleCell>)

Show an Object

updateObject(<bcbioSingleCell>)

Update an Object to Its Current Class Definition

Read Functions

readCellRanger()

Read 10X Genomics Cell Ranger Data

Data Functions

aggregateReplicates(<bcbioSingleCell>)

Aggregate Replicates

cell2sample()

Cell to Sample Mappings

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

Sample Data

selectSamples(<SingleCellExperiment>)

Select Samples

subsetPerSample()

Subset Per Sample

topBarcodes()

Top Barcodes

Quality Control Functions

barcodeRanksPerSample()

Barcode Ranks per Sample

filterCells()

Filter Cells

metrics(<SingleCellExperiment>)

Sample Barcode Metrics

metricsPerSample()

Metrics per Sample

plotBarcodeRanks()

Plot Barcode Ranks

plotCellCounts()

Plot Cell Counts

plotGenesPerCell()

Plot Genes per Cell

plotMitoRatio()

Plot Mitochondrial Transcript Abundance

plotMitoVsCoding()

Plot Mitochondrial vs. Coding Counts

plotNovelty()

Plot Novelty Score

plotQC(<SingleCellExperiment>)

Quality Control Plots

plotReadsPerCell()

Plot Read Counts per Cell

plotUMIsPerCell()

Plot UMIs per Cell

plotUMIsVsGenes()

Plot UMI and Gene Correlation

plotZerosVsDepth()

Plot Percentage of Zeros vs. Library Depth

R Markdown Functions

prepareSingleCellTemplate()

Prepare Single-Cell RNA-Seq R Markdown Template

Example Data

cellranger_small

Cell Ranger Example

indrops_small

inDrops Example