SingleCellExperiment
This is the released version of SingleCellExperiment; for the devel version, see SingleCellExperiment.
All Bioconductor versions of SingleCellExperiment
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6
S4 Classes for Single Cell Data
Bioconductor version: 3.23 · Package version: 1.34.0
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] (ORCID: 
, github: lazappi)
Maintainer: Davide Risso <risso.davide at gmail.com>
Citation
From within R, enter citation("SingleCellExperiment"):
Aaron Lun, Davide Risso. SingleCellExperiment: S4 Classes for Single Cell Data. doi:10.18129/B9.bioc.SingleCellExperiment, R package version 1.34.0, https://bioconductor.org/packages/SingleCellExperiment.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SingleCellExperiment")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.34.0 |
| License | GPL-3 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.6 (R-3.4) (8 years) |
| Downloads rank | 41 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, DataRepresentation, ImmunoOncology, Infrastructure, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/SingleCellExperiment/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SingleCellExperiment")| An introduction to the SingleCellExperiment class | HTML | R Script |
| Applying a function over a SingleCellExperiment's contents | HTML | R Script |
| Developing around the SingleCellExperiment class | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | SingleCellExperiment_1.34.0.tar.gz |
| Windows binary (x86_64) | SingleCellExperiment_1.34.0.zip |
| macOS binary (arm64) | SingleCellExperiment_1.34.0.tgz |
| macOS binary (x86_64) | SingleCellExperiment_1.34.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SingleCellExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SingleCellExperiment |
| Package Downloads Report | Download Stats |
Dependencies
Depends: SummarizedExperiment
Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray
Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne
Reverse dependencies
Depends On Me (74): alabaster.sce, BASiCS, batchelor, BayesSpace, CATALYST, celda, CellBench, CelliD, CellTrails, CHETAH, chevreulPlot, chevreulProcess, chevreulShiny, clusterExperiment, cydar, cytomapper, DeeDeeExperiment, demuxSNP, DIscBIO, dreamlet, DropletUtils, epiregulon, epiregulon.extra, ExperimentSubset, GraphExperiment, HCAData, imcdatasets, imcExperiment, iSEE, iSEEhub, iSEEindex, karyotapR, LoomExperiment, MAST, mia, MouseAgingData, MouseGastrulationData, MouseThymusAgeing, mumosa, muscData, omicsGMF, POWSC, scAnnotatR, scATAC.Explorer, scater, scDataviz, scDblFinder, scGPS, schex, scMultiome, scPipe, scran, scRNAseq, scuttle, scviR, simPIC, SingleCellAlleleExperiment, singleCellTK, SiPSiC, SpatialExperiment, splatter, STexampleData, switchde, TENxBrainData, TENxIO, TENxPBMCData, tidySingleCellExperiment, TMExplorer, TrajectoryUtils, TreeSummarizedExperiment, tricycle, TSCAN, WeberDivechaLCdata, zinbwave
Imports Me (182): ADImpute, aggregateBioVar, airpart, alabaster.sfe, anansi, anglemania, APL, ASURAT, atacInferCnv, Banksy, BASiCStan, BatChef, bayNorm, blase, BUSseq, CARDspa, CatsCradle, ccfindR, ccImpute, CDI, CellMentor, CellMixS, Cepo, ChromSCape, CiteFuse, ClusterFoldSimilarity, ClusterGVis, clustifyr, clustSIGNAL, CoGAPS, concordexR, condiments, Coralysis, corral, COTAN, crumblr, CTexploreR, CuratedAtlasQueryR, cytofQC, cytoviewer, dandelionR, decontX, DeconvoBuddies, destiny, DifferentialRegulation, Dino, distinct, dittoSeq, DOtools, EMTscoreData, escheR, EWCE, FEAST, fishpond, FLAMES, ggsc, ggspavis, glmGamPoi, GloScope, GSVA, HCATonsilData, HIPPO, Ibex, ILoReg, imageFeatureTCGA, imcRtools, immApex, immLynx, infercnv, iSEEfier, iSEEtree, iSEEu, lemur, lisaClust, looking4clusters, mastR, mbkmeans, MEB, MerfishData, MetaNeighbor, miaDash, miaTime, miaViz, mikropml, miloR, miQC, mist, mixhvg, MPAC, MuData, muscat, Nebulosa, netSmooth, NewWave, nnSVG, partCNV, peco, pipeComp, projectR, raer, raerdata, RCSL, RegionalST, RUCova, SanityR, SC3, scafari, SCArray, scBFA, scCB2, sccomp, scDD, scDDboost, scDesign3, scDiagnostics, scDotPlot, scds, scGraphVerse, scHOT, scider, SCIntRuler, scLang, sclValid, scmap, scMerge, scMET, SCnorm, scone, scp, scpdata, scQTLtools, scReClassify, scRepertoire, scRNAseqApp, scROSHI, scruff, scry, scTensor, scTGIF, scTreeViz, SETA, shinyDSP, singIST, SingleCellMultiModal, slalom, slingshot, sosta, Spaniel, SpaNorm, SpatialExperimentIO, SpatialFeatureExperiment, spatialHeatmap, spatialLIBD, speckle, spicyR, SplineDV, SpNeigh, SPOTlight, SpotSweeper, SPsimSeq, standR, StatescopeR, Statial, stPipe, SVP, TabulaMurisSenisData, tidySpatialExperiment, tpSVG, tradeSeq, treekoR, UCell, VAExprs, VDJdive, velociraptor, VisiumIO, visiumStitched, Voyager, waddR, xCell2, XeniumIO, xenLite, zellkonverter
Suggests Me (74): ANCOMBC, anndataR, bioIOT, Canek, cellxgenedp, clustree, CTdata, cudaverse, CytoSimplex, DEsingle, dominoSignal, dorothea, DuoClustering2018, dyngen, escape, ExperimentHub, FuseSOM, futurize, gedi2, genomicInstability, GEOquery, ggmlR, GSE103322, harf, harmony, hca, HDF5Array, HVP, InteractiveComplexHeatmap, jazzPanda, lstar, M3Drop, microbiomeDataSets, microSTASIS, MOFA2, MOSim, nebula, nemoR, ontoProc, phenopath, PIUMA, presto, progeny, QFeatures, RaceID, radEmu, RankMap, ReactomeGSA, rliger, scBubbletree, scConform, scFeatureFilter, scFlex, scLANE, scPassport, scPCA, scrapper, scToppR, scTypeEval, Seqtometry, Seurat, simpleSingleCell, singleCellHaystack, SingleR, sketchR, SummarizedExperiment, SuperCell, SuperCellCyto, SVG, TabulaMurisData, tidydr, tidytof, TREG, updateObject