DOI: 10.18129/B9.bioc.SingleCellExperiment  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SingleCellExperiment.

S4 Classes for Single Cell Data

Bioconductor version: 3.16

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>

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


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HTML R Script 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
PDF   Reference Manual
Text   NEWS


biocViews DataImport, DataRepresentation, ImmunoOncology, Infrastructure, SingleCell, Software
Version 1.20.1
In Bioconductor since BioC 3.6 (R-3.4) (5.5 years)
License GPL-3
Depends SummarizedExperiment
Imports methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray
Suggests testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq(>= 2.9.1), Rtsne
Depends On Me BASiCS, batchelor, BayesSpace, CATALYST, celda, CellBench, CelliD, CellTrails, CHETAH, clusterExperiment, cydar, cytomapper, DropletUtils, ExperimentSubset, HCAData, imcdatasets, iSEE, iSEEhub, LoomExperiment, MAST, mia, MouseGastrulationData, MouseThymusAgeing, mumosa, muscData, NeuCA, POWSC, scAlign, scAnnotatR, scATAC.Explorer, scater, scDataviz, scDblFinder, scGPS, schex, scPipe, scran, scRNAseq, scuttle, singleCellTK, 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, CellMixS, Cepo, ChromSCape, CiteFuse, clustifyr, CoGAPS, conclus, condiments, corral, destiny, DifferentialRegulation, Dino, distinct, dittoSeq, escape, EWCE, fcoex, FEAST, fishpond, FLAMES, ggspavis, glmGamPoi, GSVA, HIPPO, ILoReg, imcRtools, infercnv, IRISFGM, iSEEu, LineagePulse, lisaClust, mbkmeans, MetaNeighbor, miloR, miQC, MuData, muscat, Nebulosa, netSmooth, NewWave, nnSVG, peco, phemd, pipeComp, SC3, SCArray, scBFA, scCB2, sccomp, scDD, scDDboost, scds, scHOT, scmap, scMerge, scMET, SCnorm, scone, scp, scpdata, scReClassify, scRepertoire, scruff, scry, scTensor, scTGIF, scTreeViz, SingleCellMultiModal, slalom, slingshot, Spaniel, SpatialFeatureExperiment, spatialHeatmap, spatialLIBD, spicyR, SPOTlight, SPsimSeq, standR, Statial, TabulaMurisSenisData, tradeSeq, traviz, treekoR, UCell, VAExprs, VDJdive, velociraptor, Voyager, waddR, zellkonverter
Suggests Me ccImpute, CellaRepertorium, cellxgenedp, DEsingle, dorothea, DuoClustering2018, FCBF, FuseSOM, genomicInstability, GSE103322, hca, HDF5Array, InteractiveComplexHeatmap, M3Drop, microbiomeDataSets, MOFA2, ontoProc, phenopath, progeny, QFeatures, scBubbletree, scFeatureFilter, scPCA, scRecover, simpleSingleCell, SingleR, TabulaMurisData, TREG
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