SingleCellExperiment

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

All versions

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: 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")):

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.

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	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, 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	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	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
Links To Me
Build Report	Build Report, r-universe

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
Package Short Url	https://bioconductor.org/packages/SingleCellExperiment/
Package Downloads Report	Download Stats