Package: SingleR 2.15.1

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_2.15.1.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SingleR/json (API)

# Install 'SingleR' in R:

install.packages('SingleR', repos = c('https://bioc.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

12.40 score 204 stars 3 packages 3.8k scripts 97 mentions 25 exports 20 dependencies

Last updated from:2ac2314a39. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	520
linux-devel-arm64	NOTE	568
linux-devel-x86_64	NOTE	731
source / vignettes	OK	827
linux-release-arm64	NOTE	612
linux-release-x86_64	NOTE	647
macos-release-arm64	NOTE	346
macos-release-x86_64	NOTE	793
macos-oldrel-arm64	NOTE	417
macos-oldrel-x86_64	NOTE	787
windows-devel	NOTE	1669
windows-release	NOTE	1764
windows-oldrel	NOTE	1736
wasm-release	OK	1083

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

Rendered fromSingleR.Rmdusingknitr::rmarkdown

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