SingleR
This is the released version of SingleR; for the devel version, see SingleR.
Reference-Based Single-Cell RNA-Seq Annotation
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 |
Details
| biocViews | Annotation, Classification, Clustering, GeneExpression, SingleCell, Software, Transcriptomics |
| Version | 2.14.1 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | GPL-3 |
| Depends | SummarizedExperiment |
| Imports | methods, Matrix, BiocGenerics, S4Vectors, DelayedArray, stats, utils, Rcpp, beachmat(>= 2.27.3) |
| 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, BiocParallel, SingleCellExperiment, scrapper(>= 1.5.16), scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex |
| Linking To | Rcpp, beachmat, assorthead(>= 1.3.5) |
| Enhances | |
| Depends On Me | OSCA.advanced, OSCA.basic, OSCA.multisample, OSCA.workflows, SingleRBook |
| Imports Me | CellMentor, scTypeEval, singleCellTK, OSTA |
| Suggests Me | Coralysis, scDiagnostics, scGraphVerse, sketchR, tidySingleCellExperiment |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SingleR_2.14.1.tar.gz |
| Windows Binary (x86_64) | SingleR_2.14.1.zip |
| macOS Binary (big-sur-x86_64) | SingleR_2.14.1.tgz |
| macOS Binary (sonoma-arm64) | SingleR_2.14.1.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 |
| Old Source Packages for BioC 3.23 | Source Archive |