SingleR

DOI: 10.18129/B9.bioc.SingleR    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see SingleR.

Reference-Based Single-Cell RNA-Seq Annotation

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Annotating scRNA-seq data
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Annotation, Classification, Clustering, GeneExpression, SingleCell, Software, Transcriptomics
Version	1.6.1
In Bioconductor since	BioC 3.10 (R-3.6) (2 years)
License	GPL-3 + file LICENSE
Depends	SummarizedExperiment
Imports	methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocNeighbors, BiocParallel, BiocSingular, stats, utils, Rcpp, beachmat, parallel
LinkingTo	Rcpp, beachmat
Suggests	testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex
SystemRequirements	C++11
Enhances
URL	https://github.com/LTLA/SingleR
BugReports	https://support.bioconductor.org/
Depends On Me	OSCA.advanced, OSCA.basic, OSCA.multisample, OSCA.workflows
Imports Me	singleCellTK
Suggests Me	tidySingleCellExperiment
Links To Me
Build Report

Package Archives

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

Source Package	SingleR_1.6.1.tar.gz
Windows Binary	SingleR_1.6.1.zip
macOS 10.13 (High Sierra)	SingleR_1.6.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SingleR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SingleR
Package Short Url	https://bioconductor.org/packages/SingleR/
Package Downloads Report	Download Stats