# Reference-Based Single-Cell RNA-Seq Annotation

## Documentation for package ‘SingleR’ version 1.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.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