RankMap
This is the development version of RankMap; to use it, please install the devel version of Bioconductor.
Rank-based reference mapping for fast and robust cell type annotation in spatial and single-cell transcriptomics
Bioconductor version: Development (3.23)
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.
Author: Jinming Cheng [aut, cre]
Maintainer: Jinming Cheng <jinming.cheng at outlook.com>
citation("RankMap")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("RankMap")
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("RankMap")| Getting Started with RankMap | HTML | R Script |
| Reference Manual |
Details
| biocViews | Annotation, GeneExpression, Preprocessing, Regression, SingleCell, Software, Spatial, Transcriptomics |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | GPL (>= 3) |
| Depends | R (>= 4.6.0) |
| Imports | dplyr, glmnet, graphics, magrittr, Matrix, matrixStats, rlang, Seurat, stats, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/jinming-cheng/RankMap |
| Bug Reports | https://github.com/jinming-cheng/RankMap/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, SingleCellExperiment, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RankMap_0.99.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | RankMap_0.99.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RankMap |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RankMap |
| Bioc Package Browser | https://code.bioconductor.org/browse/RankMap/ |
| Package Short Url | https://bioconductor.org/packages/RankMap/ |
| Package Downloads Report | Download Stats |