CARDspa
This is the released version of CARDspa; for the devel version, see CARDspa.
All Bioconductor versions of CARDspa
3.24 (devel), 3.23 (release), 3.22, 3.21
Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics
Bioconductor version: 3.23 · Package version: 1.4.0
CARD is a reference-based deconvolution method that estimates cell type composition in spatial transcriptomics based on cell type specific expression information obtained from a reference scRNA-seq data. A key feature of CARD is its ability to accommodate spatial correlation in the cell type composition across tissue locations, enabling accurate and spatially informed cell type deconvolution as well as refined spatial map construction. CARD relies on an efficient optimization algorithm for constrained maximum likelihood estimation and is scalable to spatial transcriptomics with tens of thousands of spatial locations and tens of thousands of genes.
Author: Ying Ma [aut], Jing Fu [cre]
Maintainer: Jing Fu <jing_fu at brown.edu>
Citation
From within R, enter citation("CARDspa"):
Ying Ma. CARDspa: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics. doi:10.18129/B9.bioc.CARDspa, R package version 1.4.0, https://bioconductor.org/packages/CARDspa.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CARDspa")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.4.0 |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/YMa-lab/CARDspa |
| Bug Reports | https://github.com/YMa-lab/CARDspa/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1 year) |
| Downloads rank | 1575 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | SingleCell, Software, Spatial, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/CARDspa/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CARDspa")| Example_Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | CARDspa_1.4.0.tar.gz |
| Windows binary (x86_64) | CARDspa_1.4.0.zip |
| macOS binary (arm64) | CARDspa_1.4.0.tgz |
| macOS binary (x86_64) | CARDspa_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CARDspa |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CARDspa |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.3.0)
Imports: Rcpp (>= 1.0.7), RcppArmadillo, SummarizedExperiment, methods, MCMCpack, fields, wrMisc, concaveman, sp, dplyr, sf, Matrix, RANN, ggplot2, reshape2, RColorBrewer, S4Vectors, scatterpie, grDevices, ggcorrplot, stats, nnls, BiocParallel, NMF, spatstat.random, gtools, SingleCellExperiment, SpatialExperiment
LinkingTo: Rcpp, RcppArmadillo