original ) (raw )This is the released version of SingleCellExperiment; for the devel version, seeSingleCellExperiment .
Bioconductor version: Release (3.21)
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: , github: lazappi)
Maintainer: Davide Risso <risso.davide at gmail.com>
Citation (from within R, enter citation("SingleCellExperiment")):
To install this package, start R (version "4.5") 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 .
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
biocViews
DataImport , DataRepresentation , ImmunoOncology , Infrastructure , SingleCell , Software
Version
1.30.0
In Bioconductor since
BioC 3.6 (R-3.4) (7.5 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 , chevreulShiny , clusterExperiment , cydar , cytomapper , demuxSNP , dreamlet , DropletUtils , epiregulon , epiregulon.extra , ExperimentSubset , iSEE , iSEEhub , iSEEindex , LoomExperiment , lute , MAST , mia , mumosa , 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 , APL , ASURAT , Banksy , BASiCStan , bayNorm , BUSseq , CARDspa , CatsCradle , ccfindR , ccImpute , CDI , CellMixS , Cepo , ChromSCape , CiteFuse , ClusterFoldSimilarity , clustifyr , clustSIGNAL , CoGAPS , concordexR , condiments , corral , COTAN , crumblr , CTexploreR , CuratedAtlasQueryR , cytofQC , cytoviewer , dandelionR , decontX , DeconvoBuddies , destiny , DifferentialRegulation , Dino , distinct , dittoSeq , escape , escheR , EWCE , FEAST , fishpond , FLAMES , ggsc , ggspavis , glmGamPoi , GloScope , GSVA , HIPPO , ILoReg , imcRtools , immApex , infercnv , iSEEfier , iSEEtree , iSEEu , lemur , lisaClust , mastR , mbkmeans , MEB , MetaNeighbor , miaDash , miaViz , miloR , miQC , mist , MPAC , MuData , muscat , Nebulosa , netSmooth , NewWave , nnSVG , partCNV , peco , pipeComp , projectR , raer , RCSL , RegionalST , RUCova , SC3 , SCArray , scBFA , scCB2 , sccomp , scDD , scDDboost , scDesign3 , scDiagnostics , scDotPlot , scds , scHOT , scmap , scMerge , scMET , SCnorm , scone , scp , scQTLtools , scReClassify , scRepertoire , scRNAseqApp , scruff , scry , scTensor , scTGIF , scTreeViz , shinyDSP , slalom , slingshot , sosta , Spaniel , SpaNorm , SpatialExperimentIO , SpatialFeatureExperiment , spatialHeatmap , speckle , spicyR , SplineDV , SPOTlight , SpotSweeper , SPsimSeq , standR , Statial , SVP , tidySpatialExperiment , tpSVG , tradeSeq , treekoR , UCell , VAExprs , VDJdive , velociraptor , VisiumIO , visiumStitched , Voyager , waddR , xCell2 , XeniumIO , xenLite , zellkonverter , HCATonsilData , MerfishData , raerdata , scpdata , SingleCellMultiModal , spatialLIBD , TabulaMurisSenisData , mixhvg , nebula , SC.MEB , SCIntRuler , SCRIP , scROSHI , SpatialDDLS
Suggests Me
ANCOMBC , cellxgenedp , CTdata , DEsingle , dominoSignal , FuseSOM , genomicInstability , hca , HDF5Array , InteractiveComplexHeatmap , jazzPanda , M3Drop , microSTASIS , MOFA2 , MOSim , ontoProc , phenopath , progeny , QFeatures , ReactomeGSA , scBubbletree , scFeatureFilter , scPCA , scrapper , scRecover , SingleR , sketchR , SummarizedExperiment , tidytof , TREG , updateObject , dorothea , DuoClustering2018 , GSE103322 , microbiomeDataSets , TabulaMurisData , simpleSingleCell , Canek , clustree , CytoSimplex , dyngen , harmony , Platypus , RaceID , SCdeconR , SCORPIUS , Seurat , singleCellHaystack , SuperCell , tidydr
Links To Me
Build Report
Build Report
Follow Installation instructions to use this package in your R session.
ORCID: 0000-0001-7744-8565 , github: lazappi)