SingleR
This is thereleased version of SingleR; for the devel version, seeSingleR.
Reference-Based Single-Cell RNA-Seq Annotation
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("SingleR")For older versions of R, please refer to the appropriateBioconductor 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 | 2.12.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (6 years) |
| License | GPL-3 |
| Depends | SummarizedExperiment |
| Imports | methods,Matrix,S4Vectors,DelayedArray,DelayedMatrixStats,BiocParallel,BiocNeighbors, stats, utils,Rcpp,beachmat(>= 2.25.1) |
| 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(>= 1.3.14),scRNAseq,ggplot2,pheatmap, grDevices,gridExtra,viridis,celldex |
| Linking To | Rcpp,beachmat,assorthead(>= 1.3.5),BiocNeighbors |
| Enhances | |
| Depends On Me | OSCA.advanced, OSCA.basic, OSCA.multisample, OSCA.workflows, SingleRBook |
| Imports Me | singleCellTK, OSTA,scPipeline |
| Suggests Me | Coralysis,scDiagnostics,scGraphVerse,sketchR,tidySingleCellExperiment |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | SingleR_2.12.0.tar.gz |
| Windows Binary (x86_64) | SingleR_2.12.0.zip (64-bit only) |
| macOS Binary (x86_64) | SingleR_2.12.0.tgz |
| macOS Binary (arm64) | SingleR_2.12.0.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 |