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SingleR

Reference-Based Single-Cell RNA-Seq Annotation

Bioconductor version: 3.23 · Package version: 2.14.1

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SingleR")

Details

MaintainerAaron Lun <infinite.monkeys.with.keyboards@gmail.com>
AuthorDvir Aran [aut, cph], Aaron Lun [ctb, cre], Daniel Bunis [ctb], Jared Andrews [ctb], Friederike Dündar [ctb]
LicenseGPL-3
URLhttps://github.com/SingleR-inc/SingleR
Bug Reportshttps://github.com/SingleR-inc/SingleR/issues
System RequirementsC++17
Downloads rank6073
Source branchRELEASE_3_23
biocViewsAnnotation, Classification, Clustering, GeneExpression, SingleCell, Software, Transcriptomics

Documentation

Download

Dependencies

Depends: SummarizedExperiment

Imports: methods, Matrix, BiocGenerics, S4Vectors, DelayedArray, stats, utils, Rcpp, beachmat (>= 2.27.3)

LinkingTo: Rcpp, beachmat, assorthead (>= 1.3.5)

Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocParallel, SingleCellExperiment, scrapper (>= 1.5.16), scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex

Reverse dependencies

Imports Me (3): CellMentor, scTypeEval, singleCellTK

Suggests Me (5): Coralysis, scDiagnostics, scGraphVerse, sketchR, tidySingleCellExperiment