| .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 |