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Bioconductor - SingleR

SingleR

This is the released version of SingleR; for the devel version, see SingleR.

Reference-Based Single-Cell RNA-Seq Annotation

Bioconductor version: Release (3.21)

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.

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

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Citation (from within R, enter citation("SingleR")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SingleR")

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("SingleR")
Details biocViews Annotation, Classification, Clustering, GeneExpression, SingleCell, Software, Transcriptomics Version 2.10.0 In Bioconductor since BioC 3.10 (R-3.6) (5.5 years) License GPL-3 Depends SummarizedExperiment Imports methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocNeighbors, stats, utils, Rcpp, beachmat(>= 2.23.5) System Requirements C++17 URL https://github.com/SingleR-inc/SingleR Bug Reports https://github.com/SingleR-inc/SingleR/issues See More Suggests testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scrapper, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex Linking To Rcpp, beachmat, assorthead, BiocNeighbors Enhances Depends On Me OSCA.advanced, OSCA.basic, OSCA.multisample, OSCA.workflows, SingleRBook Imports Me singleCellTK, scPipeline Suggests Me scDiagnostics, sketchR, tidySingleCellExperiment, tidyseurat Links To Me Build Report Build Report Package Archives

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

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