# Reference-Based Single-Cell RNA-Seq Annotation

## Documentation for package ‘SingleR’ version 2.11.3

- 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 | Reference dataset extractors
classifySingleR | Classify cells with SingleR
combineCommonResults | Combine SingleR results with recomputation
combineRecomputedResults | Combine SingleR results with recomputation
configureMarkerHeatmap | Plot a heatmap of the markers for a label
DatabaseImmuneCellExpressionData | Reference dataset extractors
datasets | Reference dataset extractors
getClassicMarkers | Get classic markers
getDeltaFromMedian | Compute the difference from median
HumanPrimaryCellAtlasData | Reference dataset extractors
ImmGenData | Reference dataset extractors
matchReferences | Match labels from two references
MonacoImmuneData | Reference dataset extractors
MouseRNAseqData | Reference dataset extractors
NovershternHematopoieticData | Reference dataset extractors
plotDeltaDistribution | Plot delta distributions
plotMarkerHeatmap | Plot a heatmap of the markers for a label
plotScoreDistribution | Plot score distributions
plotScoreHeatmap | Plot a score heatmap
pruneScores | Prune out low-quality assignments
rebuildIndex | Rebuild the index
SingleR | Annotate scRNA-seq data
trainSingleR | Train the SingleR classifier