SingleR

DOI: 10.18129/B9.bioc.SingleR    

Reference-Based Single-Cell RNA-Seq Annotation

Bioconductor version: Release (3.10)

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 D√ľndar [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 "3.6") 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   LICENSE

Details

biocViews Annotation, Classification, Clustering, GeneExpression, SingleCell, Software, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License GPL-3 + file LICENSE
Depends SummarizedExperiment
Imports methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocNeighbors, BiocParallel, stats, utils, Rcpp, ExperimentHub
LinkingTo Rcpp, beachmat
Suggests testthat, knitr, rmarkdown, BiocStyle, beachmat, SingleCellExperiment, scater, scRNAseq, scran, BiocGenerics, ggplot2, pheatmap, grDevices
SystemRequirements C++11
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package SingleR_1.0.0.tar.gz
Windows Binary SingleR_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) SingleR_1.0.0.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

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