This package is for version 3.14 of Bioconductor;
for the stable, up-to-date release version, see
SingleCellExperiment.
S4 Classes for Single Cell Data
Bioconductor version: 3.14
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]
Maintainer: Davide Risso <risso.davide at gmail.com>
Citation (from within R, enter citation("SingleCellExperiment")):
Installation
To install this package, start R (version "4.1") 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.
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
Details
Version
1.16.0
In Bioconductor since
BioC 3.6 (R-3.4) (6.5 years)
License
GPL-3
System Requirements
See More
Linking To
Enhances
Depends On Me
BASiCS,
batchelor,
BayesSpace,
CATALYST,
CellBench,
CelliD,
CellTrails,
CHETAH,
clusterExperiment,
cydar,
cytomapper,
DropletUtils,
ExperimentSubset,
HCAData,
imcdatasets,
iSEE,
LoomExperiment,
MAST,
mia,
MouseGastrulationData,
MouseThymusAgeing,
mumosa,
muscData,
NeuCA,
POWSC,
scAlign,
scAnnotatR,
scATAC.Explorer,
scater,
scClassifR,
scDataviz,
scGPS,
schex,
scPipe,
scran,
scRNAseq,
scuttle,
singleCellTK,
SpatialExperiment,
splatter,
switchde,
TENxBrainData,
TENxPBMCData,
tidySingleCellExperiment,
TMExplorer,
TrajectoryUtils,
TreeSummarizedExperiment,
tricycle,
TSCAN,
zinbwave
Imports Me
ADImpute,
aggregateBioVar,
airpart,
bayNorm,
BEARscc,
BUSseq,
ccfindR,
celda,
CellMixS,
Cepo,
ChromSCape,
CiteFuse,
clustifyr,
CoGAPS,
conclus,
condiments,
corral,
destiny,
Dino,
distinct,
dittoSeq,
escape,
fcoex,
FEAST,
fishpond,
FLAMES,
ggspavis,
GSVA,
HIPPO,
ILoReg,
imcRtools,
infercnv,
IRISFGM,
iSEEu,
LineagePulse,
mbkmeans,
MetaNeighbor,
miloR,
miQC,
muscat,
Nebulosa,
netSmooth,
NewWave,
peco,
phemd,
pipeComp,
SC3,
SCArray,
scBFA,
scCB2,
scDblFinder,
scDD,
scds,
scHOT,
scmap,
scMerge,
SCnorm,
scone,
scp,
scpdata,
scReClassify,
scruff,
scry,
scTensor,
scTGIF,
scTreeViz,
SingleCellMultiModal,
slalom,
slingshot,
Spaniel,
spatialLIBD,
SPsimSeq,
TabulaMurisSenisData,
tradeSeq,
traviz,
treekoR,
VAExprs,
velociraptor,
waddR,
zellkonverter
Suggests Me
CellaRepertorium,
DEsingle,
dorothea,
DuoClustering2018,
EWCE,
FCBF,
genomicInstability,
GSE103322,
hca,
HDF5Array,
InteractiveComplexHeatmap,
M3Drop,
microbiomeDataSets,
mistyR,
MOFA2,
ontoProc,
phenopath,
progeny,
PubScore,
QFeatures,
scFeatureFilter,
scPCA,
scRecover,
simpleSingleCell,
SingleR,
TabulaMurisData
Links To Me
Package Archives
Follow Installation instructions to use this package in your R session.
Source Repository
git clone https://git.bioconductor.org/packages/SingleCellExperiment
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/SingleCellExperiment