This is the development version of CARDspa; for the stable release version, see CARDspa.
Spatially Informed Cell Type Deconvolution for Spatial TranscriptomicsBioconductor version: Development (3.22)
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, entercitation("CARDspa")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("CARDspa")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CARDspa")Follow Installation instructions to use this package in your R session.
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