SingleCellExperiment
S4 Classes for Single Cell Data
Bioconductor version: 3.24 · Package version: 1.35.2
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SingleCellExperiment")Details
| Maintainer | Davide Risso <risso.davide@gmail.com> |
| Author | Aaron Lun [aut, cph], Davide Risso [aut, cre, cph], Keegan Korthauer [ctb], Kevin Rue-Albrecht [ctb], Luke Zappia [ctb] (ORCID: <https://orcid.org/0000-0001-7744-8565>, github: lazappi) |
| License | GPL-2 | GPL-3 |
| URL | https://github.com/drisso/SingleCellExperiment |
| Bug Reports | https://github.com/drisso/SingleCellExperiment/issues |
| Downloads rank | 22784 |
| Source branch | devel |
| biocViews | DataImport, DataRepresentation, ImmunoOncology, Infrastructure, SingleCell, Software |
Documentation
- An introduction to the SingleCellExperiment class
- Applying a function over a SingleCellExperiment's contents
- Developing around the SingleCellExperiment class
Download
Follow the installation instructions to use this package in your R session.
| Source package | SingleCellExperiment_1.35.2.tar.gz |
| Windows binary (x86_64) | SingleCellExperiment_1.35.2.zip |
| macOS binary (arm64) | SingleCellExperiment_1.35.2.tgz |
| macOS binary (x86_64) | SingleCellExperiment_1.35.2.tgz |
Dependencies
Depends: SummarizedExperiment
Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray
Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne
Reverse dependencies
Depends On Me (72): alabaster.sce, BASiCS, batchelor, BayesSpace, CATALYST, celda, CellBench, 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, simPIC, SingleCellAlleleExperiment, singleCellTK, SiPSiC, SpatialExperiment, splatter, STexampleData, switchde, TENxBrainData, TENxIO, TENxPBMCData, tidySingleCellExperiment, TMExplorer, TrajectoryUtils, TreeSummarizedExperiment, tricycle, TSCAN, WeberDivechaLCdata, zinbwave
Imports Me (194): ADImpute, aggregateBioVar, airpart, alabaster.sfe, anansi, anglemania, APL, ASURAT, atacInferCnv, Banksy, BASiCStan, BatChef, bayNorm, BiocDuckDB, blase, BUSseq, CARDspa, CatsCradle, ccfindR, ccImpute, CDI, CellMentor, CellMixS, cellNexus, Cepo, ChromSCape, CiteFuse, ClusterFoldSimilarity, ClusterGVis, clustifyr, clustSIGNAL, CoGAPS, concordexR, condiments, Coralysis, corral, COTAN, crumblr, CTexploreR, CySA, cytofQC, cytoviewer, dandelionR, decontX, DeconvoBuddies, destiny, DifferentialRegulation, Dino, distinct, dittoSeq, DOtools, EMTscoreData, escheR, EWCE, FEAST, fishash, fishpond, FLAMES, ggsc, ggspavis, glmGamPoi, GloScope, GPlinksR, GSVA, HCATonsilData, HIPPO, Ibex, ILoReg, imageFeatureTCGA, imcRtools, immApex, immLynx, infercnv, iSEEfier, iSEEtree, iSEEu, lemur, lisaClust, looking4clusters, mastR, mbkmeans, MEB, MerfishData, miaDash, miaTime, miaViz, mikropml, miloR, miQC, mist, mixhvg, MPAC, MuData, MultiAssaySpatialExperiment, muscat, Nebulosa, netSmooth, NewWave, nnSVG, peco, pipeComp, projectR, QFeaturesGUI, raer, raerdata, RCSL, RegionalST, RUCova, SanityR, SC3, scafari, SCArray, scBatchQC, scBFA, scCB2, scCertify, sccomp, scCompoundDE, scDD, scDDboost, scDesign3, scDiagnostics, scDotPlot, scds, scFastDE, 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, SpaceMarkers, Spaniel, SpaNorm, spatialdataR, SpatialExperimentIO, SpatialFeatureExperiment, spatialHeatmap, spatialLIBD, speckle, spicyR, SplineDV, SpNeigh, SPOTlight, SpotSweeper, SPsimSeq, standR, StatescopeR, Statial, stPipe, SVP, SwarnSeq, TabulaMurisSenisData, tidySpatialExperiment, tpSVG, tradeSeq, treekoR, UCell, VAExprs, VDJdive, velociraptor, VisiumIO, visiumStitched, Voyager, waddR, wSIR, xCell2, XeniumIO, xenLite, zellkonverter
Suggests Me (78): ANCOMBC, anndataR, augere.solo, BenchHub, bioIOT, Canek, cellxgenedp, clustree, CTdata, cudaverse, CytoSimplex, DAssemble, dbSequence, DEsingle, dominoSignal, DuoClustering2018, dyngen, EMTscore, escape, ExperimentHub, FuseSOM, futurize, gedi2, genomicInstability, GEOquery, ggmlR, GSE103322, harf, harmony, HDF5Array, HVP, immGLIPH, InteractiveComplexHeatmap, jazzPanda, levi, lstar, M3Drop, microbiomeDataSets, MOFA2, MOSim, nebula, nemoR, ontoProc, phenopath, PIUMA, progeny, QFeatures, RaceID, radEmu, RankMap, ReactomeGSA, rliger, S4Cartographer, savingBiocObjects, scBubbletree, scConform, scFeatureFilter, scLANE, scPassport, scPCA, scrapper, scToppR, scTypeEval, Seqtometry, Seurat, simpleSingleCell, singleCellHaystack, SingleR, sketchR, SummarizedExperiment, SuperCell, SuperCellCyto, SVG, TabulaMurisData, tidydr, tidytof, TREG, updateObject