Package: SingleCellExperiment 1.29.1

Davide Risso

SingleCellExperiment: S4 Classes for Single Cell Data

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.

Authors:Aaron Lun [aut, cph], Davide Risso [aut, cre, cph], Keegan Korthauer [ctb], Kevin Rue-Albrecht [ctb], Luke Zappia [ctb]

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SingleCellExperiment.pdf |SingleCellExperiment.html✨
SingleCellExperiment/json (API)
NEWS

# Install 'SingleCellExperiment' in R:
install.packages('SingleCellExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:SingleCellExperiment-1.29.1(bioc 3.21)SingleCellExperiment-1.28.1(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologydatarepresentationdataimportinfrastructuresinglecell

13.41 score 270 packages 14k scripts 30k downloads 36 mentions 75 exports 29 dependencies

Last updated 30 days agofrom:6ed39963de. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 09 2024
R-4.5-winNOTEDec 09 2024
R-4.5-linuxNOTEDec 09 2024
R-4.4-winNOTEDec 09 2024
R-4.4-macNOTEDec 09 2024
R-4.3-winNOTEDec 09 2024
R-4.3-macNOTEDec 09 2024

Exports:altExpaltExp<-altExpNamesaltExpNames<-altExpsaltExps<-applySCEcbindcoercecolDatacolLabelscolLabels<-colPaircolPair<-colPairNamescolPairNames<-colPairscolPairs<-combineColscountscounts<-cpmcpm<-factorDatafactorData<-featureLoadingsfeatureLoadings<-int_colDataint_colData<-int_elementMetadataint_elementMetadata<-int_metadataint_metadata<-LinearEmbeddingMatrixlogcountslogcounts<-mainExpNamemainExpName<-normcountsnormcounts<-objectVersionparallel_slot_namesrbindreduced.dim.matrixreducedDimreducedDim<-reducedDimNamesreducedDimNames<-reducedDimsreducedDims<-removeAltExpsrowDatarowPairrowPair<-rowPairNamesrowPairNames<-rowPairsrowPairs<-rowSubsetrowSubset<-sampleFactorssampleFactors<-showsimplifyToSCESingleCellExperimentsizeFactorssizeFactors<-splitAltExpsswapAltExptpmtpm<-unsplitAltExpsupdateObjectweightsweights<-

Dependencies:abindaskpassBiobaseBiocGenericscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc

An introduction to the SingleCellExperiment class

Davide Risso, Aaron Lun

Rendered fromintro.Rmdusingknitr::rmarkdownon Dec 09 2024.

Last update: 2021-01-25
Started: 2017-07-14

Applying a function over a SingleCellExperiment's contents

Aaron Lun

Rendered fromapply.Rmdusingknitr::rmarkdownon Dec 09 2024.

Last update: 2021-01-27
Started: 2021-01-25

Developing around the SingleCellExperiment class

Davide Risso and Aaron Lun

Rendered fromdevel.Rmdusingknitr::rmarkdownon Dec 09 2024.

Last update: 2021-01-25
Started: 2018-08-04

Readme and manuals

Help Manual

Help pageTopics
Alternative Experiment methods% altExp altExp,SingleCellExperiment,character-method altExp,SingleCellExperiment,missing-method altExp,SingleCellExperiment,numeric-method altExp<- altExp<-,SingleCellExperiment,character-method altExp<-,SingleCellExperiment,missing-method altExp<-,SingleCellExperiment,numeric-method altExpNames altExpNames,SingleCellExperiment-method altExpNames<- altExpNames<-,SingleCellExperiment,character-method altExps altExps,SingleCellExperiment-method altExps<- altExps<-,SingleCellExperiment-method c,SummarizedExperimentByColumn-method check complain. doesn't Dumping here, length,SummarizedExperimentByColumn-method mainExpName mainExpName,SingleCellExperiment-method mainExpName<- mainExpName<-,SingleCellExperiment,character_OR_NULL-method methods names,SummarizedExperimentByColumn-method names<-,SummarizedExperimentByColumn-method removeAltExps SEBC so that the [,SummarizedExperimentByColumn,ANY,ANY,ANY-method [<-,SummarizedExperimentByColumn,ANY,ANY,ANY-method
Applying over parts of a SingleCellExperimentapplySCE
Get or set column labelscolLabels colLabels,SingleCellExperiment-method colLabels<- colLabels<-,SingleCellExperiment-method
Column pair methodscolPair colPair,SingleCellExperiment,character-method colPair,SingleCellExperiment,missing-method colPair,SingleCellExperiment,numeric-method colPair<- colPair<-,SingleCellExperiment,character-method colPair<-,SingleCellExperiment,missing-method colPair<-,SingleCellExperiment,numeric-method colPairNames colPairNames,SingleCellExperiment-method colPairNames<- colPairNames<-,SingleCellExperiment,character-method colPairs colPairs,SingleCellExperiment-method colPairs<- colPairs<-,SingleCellExperiment-method
LEM combining methodscbind,LinearEmbeddingMatrix-method rbind,LinearEmbeddingMatrix-method
Defunct methodsclearSizeFactors clearSpikes defunct isSpike isSpike<- sizeFactorNames spikeNames
LinearEmbeddingMatrix getters/setters$,LinearEmbeddingMatrix-method $<-,LinearEmbeddingMatrix-method as.matrix,LinearEmbeddingMatrix-method dim,LinearEmbeddingMatrix-method dimnames,LinearEmbeddingMatrix-method dimnames<-,LinearEmbeddingMatrix,ANY-method dimnames<-,LinearEmbeddingMatrix-method factorData factorData,LinearEmbeddingMatrix-method factorData<- factorData<-,LinearEmbeddingMatrix-method featureLoadings featureLoadings,LinearEmbeddingMatrix-method featureLoadings<- featureLoadings<-,LinearEmbeddingMatrix-method sampleFactors sampleFactors,LinearEmbeddingMatrix-method sampleFactors<- sampleFactors<-,LinearEmbeddingMatrix-method
LinearEmbeddingMatrix classLinearEmbeddingMatrix LinearEmbeddingMatrix-class
Miscellaneous LEM methodsshow,LinearEmbeddingMatrix-method
The reduced.dim.matrix classcbind.reduced.dim.matrix rbind.reduced.dim.matrix reduced.dim.matrix reduced.dim.matrix-class [.reduced.dim.matrix
Reduced dimensions methodsreducedDim reducedDim,SingleCellExperiment,character-method reducedDim,SingleCellExperiment,missing-method reducedDim,SingleCellExperiment,numeric-method reducedDim<- reducedDim<-,SingleCellExperiment,character-method reducedDim<-,SingleCellExperiment,missing-method reducedDim<-,SingleCellExperiment,numeric-method reducedDimNames reducedDimNames,SingleCellExperiment-method reducedDimNames<- reducedDimNames<-,SingleCellExperiment,character-method reducedDims reducedDims,SingleCellExperiment-method reducedDims<- reducedDims<-,SingleCellExperiment-method
Row pair methodsc,DualSubset-method length,DualSubset-method rowPair rowPair,SingleCellExperiment,character-method rowPair,SingleCellExperiment,missing-method rowPair,SingleCellExperiment,numeric-method rowPair<- rowPair<-,SingleCellExperiment,character-method rowPair<-,SingleCellExperiment,missing-method rowPair<-,SingleCellExperiment,numeric-method rowPairNames rowPairNames,SingleCellExperiment-method rowPairNames<- rowPairNames<-,SingleCellExperiment,character-method rowPairs rowPairs,SingleCellExperiment-method rowPairs<- rowPairs<-,SingleCellExperiment-method [,DualSubset,ANY,ANY,ANY-method [<-,DualSubset,ANY,ANY,ANY-method
Get or set the row subsetrowSubset rowSubset,SingleCellExperiment-method rowSubset<- rowSubset<-,SingleCellExperiment-method
Named assay getters and setterscounts counts,SingleCellExperiment-method counts<- counts<-,SingleCellExperiment-method cpm cpm,SingleCellExperiment-method cpm<- cpm<-,SingleCellExperiment-method logcounts logcounts,SingleCellExperiment-method logcounts<- logcounts<-,SingleCellExperiment-method normcounts normcounts,SingleCellExperiment-method normcounts<- normcounts<-,SingleCellExperiment-method SCE-assays tpm tpm,SingleCellExperiment-method tpm<- tpm<-,SingleCellExperiment-method weights weights,SingleCellExperiment-method weights<- weights<-,SingleCellExperiment-method
Combining or subsetting SingleCellExperiment objectscbind,SingleCellExperiment-method combineCols,SingleCellExperiment-method rbind,SingleCellExperiment-method SCE-combine [,SingleCellExperiment,ANY,ANY,ANY-method [,SingleCellExperiment,ANY,ANY-method [,SingleCellExperiment,ANY-method [<-,SingleCellExperiment,ANY,ANY,SingleCellExperiment-method
Internal SingleCellExperiment functionscolData,SingleCellExperiment-method int_colData int_colData,SingleCellExperiment-method int_colData<- int_colData<-,SingleCellExperiment-method int_elementMetadata int_elementMetadata,SingleCellExperiment-method int_elementMetadata<- int_elementMetadata<-,SingleCellExperiment-method int_metadata int_metadata,SingleCellExperiment-method int_metadata<- int_metadata<-,SingleCellExperiment-method parallel_slot_names,SingleCellExperiment-method rowData,SingleCellExperiment-method SCE-internals
Miscellaneous SingleCellExperiment methodsobjectVersion objectVersion,SingleCellExperiment-method SCE-miscellaneous show,SingleCellExperiment-method
Simplify a list to a single SingleCellExperimentsimplifyToSCE
The SingleCellExperiment classcoerce,RangedSummarizedExperiment,SingleCellExperiment-method coerce,SummarizedExperiment,SingleCellExperiment-method SingleCellExperiment SingleCellExperiment-class
Size factor methodssizeFactors sizeFactors,SingleCellExperiment-method sizeFactors<-,SingleCellExperiment-method
Split off alternative featuressplitAltExps
LEM subsetting methods[,LinearEmbeddingMatrix,ANY,ANY,ANY-method [,LinearEmbeddingMatrix,ANY,ANY-method [,LinearEmbeddingMatrix,ANY-method [<-,LinearEmbeddingMatrix,ANY,ANY,LinearEmbeddingMatrix-method
Swap main and alternative ExperimentsswapAltExp
Unsplit the alternative experimentsunsplitAltExps
Update a SingleCellExperiment objectupdateObject updateObject,SingleCellExperiment-method