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SingleCellExperiment

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

S4 Classes for Single Cell Data


Bioconductor version: Development (3.20)

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] (, lazappi)

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

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

Installation

To install this package, start R (version "4.4") 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 1.27.2
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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, clusterExperiment, cydar, cytomapper, demuxSNP, dreamlet, DropletUtils, epiregulon, epiregulon.extra, ExperimentSubset, HCAData, imcdatasets, iSEE, iSEEhub, iSEEindex, LoomExperiment, lute, MAST, mia, MouseAgingData, MouseGastrulationData, MouseThymusAgeing, mumosa, muscData, NeuCA, 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, ANCOMBC, APL, ASURAT, Banksy, BASiCStan, bayNorm, BEARscc, BUSseq, ccfindR, CDI, CellMixS, Cepo, ChromSCape, CiteFuse, ClusterFoldSimilarity, clustifyr, CoGAPS, condiments, corral, CTexploreR, CuratedAtlasQueryR, cytofQC, cytoviewer, decontX, destiny, DifferentialRegulation, Dino, distinct, dittoSeq, escape, escheR, EWCE, FEAST, fishpond, FLAMES, ggsc, ggspavis, glmGamPoi, GloScope, GSVA, HCATonsilData, HIPPO, ILoReg, imcRtools, infercnv, iSEEfier, iSEEu, lemur, lisaClust, mastR, mbkmeans, MEB, MerfishData, MetaNeighbor, miaViz, miloR, miQC, MuData, muscat, Nebulosa, netSmooth, NewWave, nnSVG, partCNV, peco, pipeComp, raer, raerdata, RCSL, RegionalST, SC3, SCArray, scBFA, scCB2, sccomp, scDD, scDDboost, scDesign3, scds, scHOT, scmap, scMerge, scMET, SCnorm, scone, scp, scpdata, scReClassify, scRepertoire, scRNAseqApp, scruff, scry, scTensor, scTGIF, scTreeViz, SingleCellMultiModal, slalom, slingshot, Spaniel, SpatialFeatureExperiment, spatialHeatmap, spatialLIBD, speckle, spicyR, SPOTlight, SpotSweeper, SPsimSeq, standR, Statial, TabulaMurisSenisData, tidySpatialExperiment, tpSVG, tradeSeq, traviz, treekoR, UCell, VAExprs, VDJdive, velociraptor, Voyager, waddR, zellkonverter
Suggests Me ccImpute, CellaRepertorium, cellxgenedp, CTdata, DEsingle, dorothea, DuoClustering2018, FuseSOM, genomicInstability, GSE103322, hca, HDF5Array, InteractiveComplexHeatmap, M3Drop, microbiomeDataSets, microSTASIS, MOFA2, MOSim, ontoProc, phenopath, progeny, QFeatures, scBubbletree, scFeatureFilter, scPCA, scRecover, simpleSingleCell, SingleR, sketchR, TabulaMurisData, TREG, updateObject
Links To Me
Build Report Build Report

Package Archives

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

Source Package SingleCellExperiment_1.27.2.tar.gz
Windows Binary SingleCellExperiment_1.27.0.zip
macOS Binary (x86_64) SingleCellExperiment_1.27.2.tgz
macOS Binary (arm64) SingleCellExperiment_1.27.0.tgz
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