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S4 Classes for Single Cell Data

Bioconductor version: Release (3.19)

Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.

Author: Aaron Lun [aut, cph], Davide Risso [aut, cre, cph], Keegan Korthauer [ctb], Kevin Rue-Albrecht [ctb], Luke Zappia [ctb] (, lazappi)

Maintainer: Davide Risso <risso.davide at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

1. An introduction to the SingleCellExperiment class HTML R Script
2. Applying over a SingleCellExperiment object HTML R Script
3. Developing around the SingleCellExperiment class HTML R Script
Reference Manual PDF


biocViews DataImport, DataRepresentation, ImmunoOncology, Infrastructure, SingleCell, Software
Version 1.26.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3
Depends SummarizedExperiment
Imports methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray
System Requirements
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq(>= 2.9.1), Rtsne
Linking To
Depends On Me alabaster.sce, BASiCS, batchelor, BayesSpace, CATALYST, celda, CellBench, CelliD, CellTrails, CHETAH, clusterExperiment, cydar, cytomapper, demuxSNP, dreamlet, DropletUtils, epiregulon, epiregulon.extra, ExperimentSubset, iSEE, iSEEhub, iSEEindex, LoomExperiment, lute, MAST, mia, mumosa, NeuCA, POWSC, scAnnotatR, scater, scDblFinder, scGPS, schex, scPipe, scran, scuttle, scviR, simPIC, SingleCellAlleleExperiment, singleCellTK, SiPSiC, SpatialExperiment, splatter, switchde, TENxIO, tidySingleCellExperiment, TrajectoryUtils, TreeSummarizedExperiment, tricycle, TSCAN, zinbwave, HCAData, imcdatasets, MouseAgingData, MouseGastrulationData, MouseThymusAgeing, muscData, scATAC.Explorer, scMultiome, scRNAseq, STexampleData, TENxBrainData, TENxPBMCData, TMExplorer, WeberDivechaLCdata, OSCA.intro, DIscBIO, imcExperiment, karyotapR
Imports Me ADImpute, aggregateBioVar, airpart, ANCOMBC, APL, ASURAT, Banksy, BASiCStan, bayNorm, BEARscc, BUSseq, ccfindR, CDI, CellMixS, Cepo, ChromSCape, CiteFuse, ClusterFoldSimilarity, clustifyr, CoGAPS, condiments, corral, CTexploreR, CuratedAtlasQueryR, cytofQC, cytoviewer, decontX, destiny, DifferentialRegulation, Dino, distinct, dittoSeq, escape, escheR, EWCE, FEAST, fishpond, FLAMES, ggsc, ggspavis, glmGamPoi, GloScope, GSVA, HIPPO, ILoReg, imcRtools, infercnv, iSEEfier, iSEEu, lemur, lisaClust, mastR, mbkmeans, MEB, MetaNeighbor, miaViz, miloR, miQC, MuData, muscat, Nebulosa, netSmooth, NewWave, nnSVG, partCNV, peco, pipeComp, raer, RCSL, RegionalST, SC3, SCArray, scBFA, scCB2, sccomp, scDD, scDDboost, scDesign3, scds, scHOT, scmap, scMerge, scMET, SCnorm, scone, scp, scReClassify, scRepertoire, scRNAseqApp, scruff, scry, scTensor, scTGIF, scTreeViz, slalom, slingshot, Spaniel, SpatialFeatureExperiment, spatialHeatmap, speckle, spicyR, SPOTlight, SpotSweeper, SPsimSeq, standR, Statial, tidySpatialExperiment, tpSVG, tradeSeq, traviz, treekoR, UCell, VAExprs, VDJdive, velociraptor, Voyager, waddR, zellkonverter, HCATonsilData, MerfishData, raerdata, scpdata, SingleCellMultiModal, spatialLIBD, TabulaMurisSenisData, digitalDLSorteR, mixhvg, nebula, SC.MEB, SCIntRuler, SCRIP, scROSHI, SpatialDDLS
Suggests Me ccImpute, cellxgenedp, CTdata, DEsingle, FuseSOM, genomicInstability, hca, HDF5Array, InteractiveComplexHeatmap, M3Drop, microSTASIS, MOFA2, MOSim, ontoProc, phenopath, progeny, QFeatures, scBubbletree, scFeatureFilter, scPCA, scRecover, SingleR, sketchR, TREG, updateObject, dorothea, DuoClustering2018, GSE103322, microbiomeDataSets, TabulaMurisData, simpleSingleCell, Canek, clustree, CytoSimplex, dyngen, harmony, RaceID, rliger, SCdeconR, SCORPIUS, Seurat, singleCellHaystack, tidydr
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Source Package SingleCellExperiment_1.26.0.tar.gz
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macOS Binary (x86_64) SingleCellExperiment_1.26.0.tgz
macOS Binary (arm64) SingleCellExperiment_1.26.0.tgz
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