Package: SingleR 2.7.1

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]

SingleR_2.7.1.tar.gz
SingleR_2.7.1.zip(r-4.5)SingleR_2.7.1.zip(r-4.4)SingleR_2.7.1.zip(r-4.3)
SingleR_2.7.1.tgz(r-4.4-arm64)SingleR_2.7.1.tgz(r-4.4-x86_64)SingleR_2.7.1.tgz(r-4.3-arm64)SingleR_2.7.1.tgz(r-4.3-x86_64)
SingleR_2.7.1.tar.gz(r-4.5-noble)SingleR_2.7.1.tar.gz(r-4.4-noble)
SingleR_2.7.1.tgz(r-4.4-emscripten)SingleR_2.7.1.tgz(r-4.3-emscripten)
SingleR.pdf |SingleR.html✨
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/ltla/singler/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:SingleR-2.7.1(bioc 3.20)SingleR-2.6.0(bioc 3.19)

bioconductor-package

23 exports 1.69 score 47 dependencies 1 dependents 97 mentions

Last updated 2 months agofrom:84a6e55d43

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

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

Using SingleR to annotate single-cell RNA-seq data

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

Rendered fromSingleR.Rmdusingknitr::rmarkdownon Jun 24 2024.

Last update: 2024-02-14
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 common genes	combineCommonResults
Combine SingleR results with recomputation	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 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