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Bioconductor - SingleCellExperiment (development version)

SingleCellExperiment

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

S4 Classes for Single Cell Data

Bioconductor version: Development (3.22)

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")): Installation

To install this package, start R (version "4.5") 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 Details biocViews DataImport, DataRepresentation, ImmunoOncology, Infrastructure, SingleCell, Software Version 1.31.1 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, mia, mumosa, scAnnotatR, scater, scDblFinder, scGPS, schex, scPipe, scran, scuttle, scviR, simPIC, SingleCellAlleleExperiment, 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, CiteFuse, ClusterFoldSimilarity, clustifyr, clustSIGNAL, CoGAPS, concordexR, condiments, Coralysis, corral, COTAN, crumblr, CTexploreR, CuratedAtlasQueryR, cytofQC, cytoviewer, dandelionR, decontX, DeconvoBuddies, destiny, DifferentialRegulation, Dino, distinct, dittoSeq, 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, SCIntRuler, scROSHI, SpatialDDLS Suggests Me ANCOMBC, cellxgenedp, CTdata, DEsingle, dominoSignal, escape, FuseSOM, genomicInstability, hca, HDF5Array, HVP, 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, rliger, SCdeconR, SCORPIUS, Seurat, singleCellHaystack, SuperCell, tidydr Links To Me Build Report Build Report Package Archives

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