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Reference-Based Single-Cell RNA-Seq Annotation

Bioconductor version: Release (3.18)

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.

Author: Dvir Aran [aut, cph], Aaron Lun [ctb, cre], Daniel Bunis [ctb], Jared Andrews [ctb], Friederike D√ľndar [ctb]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Citation (from within R, enter citation("SingleR")):


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Annotating scRNA-seq data HTML R Script
Reference Manual PDF


biocViews Annotation, Classification, Clustering, GeneExpression, SingleCell, Software, Transcriptomics
Version 2.4.1
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-3 + file LICENSE
Depends SummarizedExperiment
Imports methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocSingular, stats, utils, Rcpp, beachmat, parallel
System Requirements C++17
URL https://github.com/LTLA/SingleR
Bug Reports https://support.bioconductor.org/
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Suggests testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex
Linking To Rcpp, beachmat, BiocNeighbors
Depends On Me OSCA.advanced, OSCA.basic, OSCA.multisample, OSCA.workflows, SingleRBook
Imports Me singleCellTK
Suggests Me tidySingleCellExperiment
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SingleR_2.4.1.tar.gz
Windows Binary SingleR_2.4.1.zip
macOS Binary (x86_64) SingleR_2.4.1.tgz
macOS Binary (arm64) SingleR_2.4.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/SingleR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SingleR
Bioc Package Browser https://code.bioconductor.org/browse/SingleR/
Package Short Url https://bioconductor.org/packages/SingleR/
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Old Source Packages for BioC 3.18 Source Archive