We developed CARDspa, a Bioconductor version of the original CARD method [https://github.com/YMa-lab/CARD], for spatially informed cell type deconvolution in spatial transcriptomics. CARDspa is a reference-based deconvolution tool that estimates the cell type composition in spatial transcriptomics data by utilizing cell-type-specific expression information obtained from reference single-cell RNA sequencing (scRNA-seq) data.
A key feature of CARDspa is its ability to accommodate spatial correlation in the cell type composition across different tissue locations, which ensures accurate and spatially informed deconvolution, as well as refined spatial map construction. This is achieved through an efficient optimization algorithm for constrained maximum likelihood estimation. CARDspa is scalable to handle spatial transcriptomics data with tens of thousands of spatial locations and genes.
As a Bioconductor package, CARDspa is designed to integrate seamlessly with other Bioconductor tools for analyzing and visualizing high-dimensional biological data. It leverages Bioconductor's robust framework for reproducibility and ease of use within the R ecosystem.
CARDspa is implemented as an open-source R package, and is freely available on Bioconductor at [https://bioconductor.org/packages/CARDspa/].
You can install the released version of CARDspa using BioConductor.
# install BiocManager if necessary
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CARDspa")
Or you can install using devtools in R.
# install devtools if necessary
install.packages('devtools')
# install the CARDspa package
devtools::install_github('https://github.com/YMa-lab/CARDspa')
# load package
library(CARDspa)
All feedback, bug reports and suggestions are warmly welcomed! Please make sure to raise issues with a detailed and reproducible exmple and also please provide the output of your sessionInfo() in R!
Ma, Y., Zhou, X. Spatially informed cell-type deconvolution for spatial transcriptomics. Nat Biotechnol 40, 1349–1359 (2022). https://doi.org/10.1038/s41587-022-01273-7
Please see vignettes.
browseVignettes("CARDspa")