Reference-Based Single-Cell RNA-Seq Annotation

Documentation for package ‘SingleR’ version 1.2.1

.mockRefData	Mock data for examples
.mockTestData	Mock data for examples
aggregateReference	Aggregate reference samples
BlueprintEncodeData	Obtain human bulk RNA-seq data from Blueprint and ENCODE
classifySingleR	Classify cells with SingleR
combine-predictions	Combining results from different references
combineCommonResults	Combine SingleR results with common genes
combineRecomputedResults	Combine SingleR results with recomputation
DatabaseImmuneCellExpressionData	Obtain human bulk RNA-seq data from DICE
getDeltaFromMedian	Compute the difference from median
HumanPrimaryCellAtlasData	Obtain the HPCA data
ImmGenData	Obtain mouse bulk expression data from the Immunologic Genome Project
matchReferences	Match labels from two references
MonacoImmuneData	Obtain bulk RNA-seq data of sorted human immune cells
MouseRNAseqData	Obtain mouse bulk expression data of sorted cell populations (RNA-seq)
NovershternHematopoieticData	Obtain bulk microarray expression for sorted hematopoietic cells
plotScoreDistribution	Plot score distributions of labels.
plotScoreHeatmap	Plot a score heatmap
pruneScores	Prune out low-quality assignments
SingleR	Annotate scRNA-seq data
trainSingleR	Train the SingleR classifier