Welcome to the new bioconductor.org!


S4 Classes for Single Cell Data

Bioconductor version: Release (3.18)

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]

Maintainer: Davide Risso <risso.davide at gmail.com>

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


To install this package, start R (version "4.3") 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 1.24.0
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, ExperimentSubset, HCAData, imcdatasets, iSEE, iSEEhub, iSEEindex, LoomExperiment, MAST, mia, MouseGastrulationData, MouseThymusAgeing, mumosa, muscData, NeuCA, POWSC, scAnnotatR, scATAC.Explorer, scater, scDataviz, scDblFinder, scGPS, schex, scMultiome, scPipe, scran, scRNAseq, scuttle, scviR, singleCellTK, SiPSiC, SpatialExperiment, splatter, switchde, TENxBrainData, TENxIO, TENxPBMCData, tidySingleCellExperiment, TMExplorer, TrajectoryUtils, TreeSummarizedExperiment, tricycle, TSCAN, WeberDivechaLCdata, zinbwave
Imports Me ADImpute, aggregateBioVar, airpart, ANCOMBC, APL, ASURAT, BASiCStan, bayNorm, BEARscc, BUSseq, ccfindR, CDI, CellMixS, Cepo, ChromSCape, CiteFuse, clustifyr, CoGAPS, condiments, corral, CuratedAtlasQueryR, cytofQC, cytoviewer, decontX, destiny, DifferentialRegulation, Dino, distinct, dittoSeq, escape, escheR, EWCE, fcoex, FEAST, fishpond, FLAMES, ggsc, ggspavis, glmGamPoi, GloScope, GSVA, HCATonsilData, HIPPO, ILoReg, imcRtools, infercnv, IRISFGM, iSEEu, lemur, LineagePulse, lisaClust, mastR, mbkmeans, MEB, MerfishData, MetaNeighbor, miaViz, miloR, miQC, MuData, muscat, Nebulosa, netSmooth, NewWave, nnSVG, partCNV, peco, phemd, pipeComp, raer, raerdata, RegionalST, SC3, SCArray, scBFA, scCB2, sccomp, scDD, scDDboost, scDesign3, scds, scHOT, scmap, scMerge, scMET, SCnorm, scone, scp, scpdata, scReClassify, scRepertoire, scRNAseqApp, scruff, scry, scTensor, scTGIF, scTreeViz, SingleCellMultiModal, slalom, slingshot, Spaniel, SpatialFeatureExperiment, spatialHeatmap, spatialLIBD, speckle, spicyR, SPOTlight, SPsimSeq, standR, Statial, TabulaMurisSenisData, tradeSeq, traviz, treekoR, UCell, VAExprs, VDJdive, velociraptor, Voyager, waddR, zellkonverter
Suggests Me ccImpute, CellaRepertorium, cellxgenedp, CTdata, DEsingle, dorothea, DuoClustering2018, FCBF, FuseSOM, genomicInstability, GSE103322, hca, HDF5Array, InteractiveComplexHeatmap, M3Drop, microbiomeDataSets, microSTASIS, MOFA2, ontoProc, phenopath, progeny, QFeatures, scBubbletree, scFeatureFilter, scPCA, scRecover, simpleSingleCell, SingleR, TabulaMurisData, TREG, updateObject
Links To Me
Build Report Build Report

Package Archives

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

Source Package SingleCellExperiment_1.24.0.tar.gz
Windows Binary SingleCellExperiment_1.24.0.zip
macOS Binary (x86_64) SingleCellExperiment_1.24.0.tgz
macOS Binary (arm64) SingleCellExperiment_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SingleCellExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SingleCellExperiment
Bioc Package Browser https://code.bioconductor.org/browse/SingleCellExperiment/
Package Short Url https://bioconductor.org/packages/SingleCellExperiment/
Package Downloads Report Download Stats