SingleR
Reference-Based Single-Cell RNA-Seq Annotation
Bioconductor version: Release (3.19)
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("SingleR")):
Installation
To install this package, start R (version "4.4") 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")| Annotating scRNA-seq data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, Classification, Clustering, GeneExpression, SingleCell, Software, Transcriptomics |
| Version | 2.6.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (5 years) |
| License | GPL-3 + file LICENSE |
| Depends | SummarizedExperiment |
| Imports | methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocSingular, stats, utils, Rcpp, beachmat, parallel |
| System Requirements | C++17 |
| URL | https://github.com/LTLA/SingleR |
| Bug Reports | https://support.bioconductor.org/ |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex |
| Linking To | Rcpp, beachmat, BiocNeighbors |
| Enhances | |
| Depends On Me | OSCA.advanced, OSCA.basic, OSCA.multisample, OSCA.workflows, SingleRBook |
| Imports Me | singleCellTK |
| Suggests Me | sketchR, tidySingleCellExperiment, tidySpatialExperiment, tidyseurat |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SingleR_2.6.0.tar.gz |
| Windows Binary (x86_64) | SingleR_2.6.0.zip |
| macOS Binary (x86_64) | SingleR_2.6.0.tgz |
| macOS Binary (arm64) | SingleR_2.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SingleR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SingleR |
| Bioc Package Browser | https://code.bioconductor.org/browse/SingleR/ |
| Package Short Url | https://bioconductor.org/packages/SingleR/ |
| Package Downloads Report | Download Stats |