SingleCellExperiment

This is the released version of SingleCellExperiment; for the devel version, see SingleCellExperiment.

S4 Classes for Single Cell Data

Bioconductor version: Release (3.23)

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: ORCID: 0000-0001-7744-8565 , github: lazappi)

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

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

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

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.

Documentation

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

browseVignettes("SingleCellExperiment")

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
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, ImmunoOncology, Infrastructure, SingleCell, Software
Version	1.34.0
In Bioconductor since	BioC 3.6 (R-3.4) (9 years)
License	GPL-3
Depends	SummarizedExperiment
Imports	methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray
System Requirements
URL

Suggests	testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq(>= 2.9.1), Rtsne
Linking To
Enhances
Depends On Me	alabaster.sce, BASiCS, batchelor, BayesSpace, CATALYST, celda, CellBench, CelliD, CellTrails, CHETAH, chevreulPlot, chevreulProcess, chevreulShiny, clusterExperiment, cydar, cytomapper, DeeDeeExperiment, demuxSNP, dreamlet, DropletUtils, epiregulon, epiregulon.extra, ExperimentSubset, GraphExperiment, iSEE, iSEEhub, iSEEindex, LoomExperiment, MAST, mia, mumosa, omicsGMF, 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, 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, escheR, EWCE, FEAST, fishpond, FLAMES, ggsc, ggspavis, glmGamPoi, GloScope, GSVA, HIPPO, Ibex, ILoReg, imageFeatureTCGA, imcRtools, immApex, immLynx, infercnv, iSEEfier, iSEEtree, iSEEu, lemur, lisaClust, looking4clusters, mastR, mbkmeans, MEB, miaDash, miaTime, miaViz, miloR, miQC, mist, MPAC, MuData, muscat, Nebulosa, netSmooth, NewWave, nnSVG, partCNV, peco, pipeComp, projectR, raer, RCSL, RegionalST, RUCova, SanityR, SC3, scafari, SCArray, scBFA, scCB2, sccomp, scDD, scDDboost, scDesign3, scDiagnostics, scDotPlot, scds, scGraphVerse, scHOT, scider, scLang, scmap, scMerge, scMET, SCnorm, scone, scp, scQTLtools, scReClassify, scRepertoire, scRNAseqApp, scruff, scry, scTensor, scTGIF, scTreeViz, SETA, shinyDSP, singIST, slalom, slingshot, sosta, Spaniel, SpaNorm, SpatialExperimentIO, SpatialFeatureExperiment, spatialHeatmap, speckle, spicyR, SplineDV, SpNeigh, SPOTlight, SpotSweeper, SPsimSeq, standR, StatescopeR, Statial, stPipe, SVP, tidySpatialExperiment, tpSVG, tradeSeq, treekoR, UCell, VAExprs, VDJdive, velociraptor, VisiumIO, visiumStitched, Voyager, waddR, xCell2, XeniumIO, xenLite, zellkonverter, EMTscoreData, HCATonsilData, MerfishData, raerdata, scpdata, SingleCellMultiModal, spatialLIBD, TabulaMurisSenisData, mikropml, mixhvg, scROSHI
Suggests Me	ANCOMBC, anndataR, cellxgenedp, CTdata, DEsingle, dominoSignal, escape, FuseSOM, genomicInstability, GEOquery, HDF5Array, HVP, InteractiveComplexHeatmap, jazzPanda, M3Drop, MOFA2, MOSim, ontoProc, phenopath, PIUMA, progeny, QFeatures, RankMap, ReactomeGSA, scBubbletree, scConform, scFeatureFilter, scLANE, scPassport, scPCA, scrapper, scRecover, scToppR, scTypeEval, Seqtometry, SingleR, sketchR, SummarizedExperiment, SuperCellCyto, TREG, updateObject, dorothea, DuoClustering2018, GSE103322, microbiomeDataSets, TabulaMurisData, simpleSingleCell, Canek, clustree, CytoSimplex, dyngen, futurize, gedi2, ggmlR, harmony, lstar, nebula, nemoR, RaceID, radEmu, rliger, Seurat, singleCellHaystack, SuperCell, SVG, tidydr
Links To Me
Build Report	Build Report

Package Archives

Follow 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 (64-bit only)
macOS Binary (big-sur-x86_64)	SingleCellExperiment_1.34.0.tgz
macOS Binary (sonoma-arm64)	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
Bioc Package Browser	https://code.bioconductor.org/browse/SingleCellExperiment/
Package Short Url	https://bioconductor.org/packages/SingleCellExperiment/
Package Downloads Report	Download Stats