Package: SingleR 2.14.0

Aaron Lun

SingleR: Reference-Based Single-Cell RNA-Seq Annotation

Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.

Authors:Dvir Aran [aut, cph], Aaron Lun [ctb, cre], Daniel Bunis [ctb], Jared Andrews [ctb], Friederike Dündar [ctb]

SingleR_2.14.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
SingleR/json (API)
NEWS

# Install 'SingleR' in R:

install.packages('SingleR', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/singler-inc/singler/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:SingleR-2.15.1(bioc 3.24)SingleR-2.14.0(bioc 3.23)

software singlecell geneexpression transcriptomics classification clustering annotation bioconductor singler cpp

13.28 score 202 stars 3 packages 4.1k scripts 7.2k downloads 97 mentions 25 exports 20 dependencies

Last updated from:a1a0ecf709 (on RELEASE_3_23). Checks:1 WARNING, 9 NOTE, 2 OK, 2 ERROR. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	294
linux-devel-arm64	NOTE	391
linux-devel-x86_64	NOTE	407
source / vignettes	OK	411
linux-release-arm64	NOTE	381
linux-release-x86_64	NOTE	439
macos-release-arm64	NOTE	268
macos-release-x86_64	NOTE	983
macos-oldrel-arm64	ERROR	335
macos-oldrel-x86_64	ERROR	504
windows-devel	NOTE	1814
windows-release	NOTE	1806
windows-oldrel	NOTE	1746
wasm-release	OK	251

Exports:.mockRefData .mockTestData aggregateReference BlueprintEncodeData classifySingleR combineCommonResults combineRecomputedResults configureMarkerHeatmap DatabaseImmuneCellExpressionData getClassicMarkers getDeltaFromMedian HumanPrimaryCellAtlasData ImmGenData matchReferences MonacoImmuneData MouseRNAseqData NovershternHematopoieticData plotDeltaDistribution plotMarkerHeatmap plotScoreDistribution plotScoreHeatmap pruneScores rebuildIndex SingleR trainSingleR

Dependencies:abind assorthead beachmat Biobase BiocGenerics DelayedArray generics GenomicRanges IRanges lattice Matrix MatrixGenerics matrixStats Rcpp S4Arrays S4Vectors Seqinfo SparseArray SummarizedExperiment XVector

Using SingleR to annotate single-cell RNA-seq data

Aaron Lun, Jared M. Andrews, Friederike Dündar, Daniel Bunis

Rendered fromSingleR.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-01-05
Started: 2019-07-12

Citation

Development and contributors

Readme and manuals

Help Manual

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