Package: SingleR 2.9.6

Aaron Lun

SingleR: Reference-Based Single-Cell RNA-Seq Annotation

Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.

Authors:Dvir Aran [aut, cph], Aaron Lun [ctb, cre], Daniel Bunis [ctb], Jared Andrews [ctb], Friederike Dündar [ctb]

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SingleR/json (API)
NEWS

# Install 'SingleR' in R:

install.packages('SingleR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/singler-inc/singler/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:SingleR-2.9.4(bioc 3.21)SingleR-2.8.0(bioc 3.20)

software singlecell geneexpression transcriptomics classification clustering annotation bioconductor singler cpp

12.60 score 182 stars 1 packages 2.1k scripts 6.2k downloads 97 mentions 25 exports 43 dependencies

Last updated 7 days agofrom:96c5041530. Checks:11 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 17 2025
R-4.5-win-x86_64	OK	Feb 17 2025
R-4.5-mac-x86_64	OK	Feb 17 2025
R-4.5-mac-aarch64	OK	Feb 17 2025
R-4.5-linux-x86_64	OK	Feb 17 2025
R-4.4-win-x86_64	OK	Feb 17 2025
R-4.4-mac-x86_64	OK	Feb 17 2025
R-4.4-mac-aarch64	OK	Feb 17 2025
R-4.3-win-x86_64	OK	Feb 17 2025
R-4.3-mac-x86_64	OK	Feb 17 2025
R-4.3-mac-aarch64	OK	Feb 17 2025

Exports:.mockRefData .mockTestData aggregateReference BlueprintEncodeData classifySingleR combineCommonResults combineRecomputedResults configureMarkerHeatmap DatabaseImmuneCellExpressionData getClassicMarkers getDeltaFromMedian HumanPrimaryCellAtlasData ImmGenData matchReferences MonacoImmuneData MouseRNAseqData NovershternHematopoieticData plotDeltaDistribution plotMarkerHeatmap plotScoreDistribution plotScoreHeatmap pruneScores rebuildIndex SingleR trainSingleR

Dependencies:abind askpass assorthead beachmat BH Biobase BiocGenerics BiocNeighbors BiocParallel codetools cpp11 crayon curl DelayedArray DelayedMatrixStats formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 Rcpp S4Arrays S4Vectors snow SparseArray sparseMatrixStats SummarizedExperiment sys UCSC.utils XVector

Using SingleR to annotate single-cell RNA-seq data

Aaron Lun, Jared M. Andrews, Friederike Dündar, Daniel Bunis

Rendered fromSingleR.Rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2024-12-11
Started: 2019-07-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Mock data for examples	.mockRefData .mockTestData
Aggregate reference samples	aggregateReference
Classify cells with SingleR	classifySingleR
Combine SingleR results with recomputation	combineCommonResults combineRecomputedResults
Reference dataset extractors	BlueprintEncodeData DatabaseImmuneCellExpressionData datasets HumanPrimaryCellAtlasData ImmGenData MonacoImmuneData MouseRNAseqData NovershternHematopoieticData
Get classic markers	getClassicMarkers
Compute the difference from median	getDeltaFromMedian
Match labels from two references	matchReferences
Plot delta distributions	plotDeltaDistribution
Plot a heatmap of the markers for a label	configureMarkerHeatmap plotMarkerHeatmap
Plot score distributions	plotScoreDistribution
Plot a score heatmap	plotScoreHeatmap
Prune out low-quality assignments	pruneScores
Rebuild the index	rebuildIndex
Annotate scRNA-seq data	SingleR
Train the SingleR classifier	trainSingleR