DOI: 10.18129/B9.bioc.SingleCellExperiment    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see SingleCellExperiment.

S4 Classes for Single Cell Data

Bioconductor version: 3.8

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]

Maintainer: Davide Risso <risso.davide at>

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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:



HTML R Script 1. An introduction to the SingleCellExperiment class
HTML R Script 2. Developing around the SingleCellExperiment class
PDF   Reference Manual
Text   NEWS


biocViews DataImport, DataRepresentation, ImmunoOncology, Infrastructure, SingleCell, Software
Version 1.4.1
In Bioconductor since BioC 3.6 (R-3.4) (1.5 years)
License GPL-3
Depends R (>= 3.5), SummarizedExperiment
Imports S4Vectors, methods, BiocGenerics, utils, stats
Suggests testthat, BiocStyle, knitr, rmarkdown, scRNAseq, magrittr, Rtsne
Depends On Me allenpvc, BASiCS, CellTrails, clusterExperiment, cydar, DropletUtils, iSEE, LoomExperiment, MAST, scater, scPipe, scran, simpleSingleCell, singleCellTK, splatter, switchde, TENxBrainData, TENxPBMCData, zinbwave
Imports Me bayNorm, BEARscc, CATALYST, ccfindR, CoGAPS, LineagePulse, netSmooth, SC3, scDD, scfind, scmap, SCnorm, scruff, slalom, slingshot
Suggests Me DEsingle, destiny, DuoClustering2018, FCBF, phenopath, scFeatureFilter, TabulaMurisData
Links To Me
Build Report  

Package Archives

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

Source Package SingleCellExperiment_1.4.1.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) SingleCellExperiment_1.4.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: