Home
Bioconductor 3.23
Software Packages
SingleCellExperiment (development version)

SingleCellExperiment

This is the development version of SingleCellExperiment; for the stable release version, see SingleCellExperiment.

S4 Classes for Single Cell Data

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.SingleCellExperiment

Bioconductor version: Development (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 iD ORCID: 0000-0001-7744-8565 , github: lazappi)

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

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

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 1.33.0

In Bioconductor since BioC 3.6 (R-3.4) (8 years)

License GPL-3

Depends SummarizedExperiment

Imports methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray

System Requirements

URL

See More

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, clusterExperiment, cydar, cytomapper, DeeDeeExperiment, demuxSNP, dreamlet, DropletUtils, epiregulon, epiregulon.extra, ExperimentSubset, 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, Banksy, BASiCStan, bayNorm, blase, BUSseq, CARDspa, CatsCradle, ccfindR, ccImpute, CDI, CellMixS, Cepo, ChromSCape, CiteFuse, ClusterFoldSimilarity, clustifyr, clustSIGNAL, CoGAPS, concordexR, condiments, Coralysis, corral, COTAN, crumblr, CTexploreR, CuratedAtlasQueryR, cytoviewer, dandelionR, decontX, DeconvoBuddies, destiny, DifferentialRegulation, Dino, distinct, dittoSeq, DOtools, escheR, EWCE, FEAST, fishpond, FLAMES, ggsc, ggspavis, glmGamPoi, GSVA, HIPPO, ILoReg, imcRtools, immApex, 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, scmap, scMerge, scMET, SCnorm, scone, scp, scReClassify, scRNAseqApp, scruff, scry, scTensor, scTGIF, scTreeViz, SETA, shinyDSP, slalom, slingshot, sosta, Spaniel, SpaNorm, SpatialExperimentIO, SpatialFeatureExperiment, speckle, spicyR, SplineDV, SPOTlight, SpotSweeper, SPsimSeq, standR, Statial, stPipe, SVP, tidySpatialExperiment, tpSVG, tradeSeq, treekoR, UCell, VAExprs, VDJdive, velociraptor, VisiumIO, visiumStitched, Voyager, waddR, xCell2, XeniumIO, xenLite, zellkonverter, HCATonsilData, MerfishData, raerdata, scpdata, SingleCellMultiModal, spatialLIBD, TabulaMurisSenisData, mikropml, mixhvg, nebula, scROSHI, SpatialDDLS

Links To Me

Build Report Build Report

Package Archives

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

Source Package SingleCellExperiment_1.33.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

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