RankMap
Rank-based reference mapping for fast and robust cell type annotation in spatial and single-cell transcriptomics
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
RankMap is a fast and scalable tool for reference-based cell type annotation of single-cell and spatial transcriptomics data. It uses ranked gene expression and multinomial regression to achieve robust predictions, even with partial gene coverage. Compatible with Seurat, SingleCellExperiment, and SpatialExperiment objects, RankMap offers flexible preprocessing and significantly faster runtime than tools like SingleR, Azimuth, and RCTD.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RankMap")Details
| Maintainer | Jinming Cheng <jinming.cheng@outlook.com> |
| Author | Jinming Cheng [aut, cre] (ORCID: <https://orcid.org/0000-0003-3806-4694>) |
| License | GPL (>= 3) |
| URL | https://github.com/jinming-cheng/RankMap |
| Bug Reports | https://github.com/jinming-cheng/RankMap/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, GeneExpression, Preprocessing, Regression, SingleCell, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/RankMap/ |
Citation
From within R, enter citation("RankMap"):
Jinming Cheng. RankMap: Rank-based reference mapping for fast and robust cell type annotation in spatial and single-cell transcriptomics. doi:10.18129/B9.bioc.RankMap, R package version 1.0.0, https://bioconductor.org/packages/RankMap.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | RankMap_1.0.0.tar.gz |
| Windows binary (x86_64) | RankMap_1.0.0.zip |
| macOS binary (arm64) | RankMap_1.0.0.tgz |
| macOS binary (x86_64) | RankMap_1.0.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: dplyr, glmnet, graphics, magrittr, Matrix, matrixStats, rlang, Seurat, stats, SummarizedExperiment
Suggests: BiocStyle, knitr, rmarkdown, SingleCellExperiment, testthat (>= 3.0.0)