Package: CARDspa
Title: Spatially Informed Cell Type Deconvolution for Spatial
        Transcriptomics
Version: 1.4.0
Date: 2025-2-6
Authors@R: 
    c(person(given = "Ying", 
    family = "Ma", 
    email = "ying_ma@brown.edu",
    role = "aut"),
    person(given = "Jing", 
    family = "Fu", 
    email = "jing_fu@brown.edu",
    role = "cre"))
Description: 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.
License: GPL-3 + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
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
LazyData: false
biocViews: Spatial, SingleCell, Transcriptomics, Visualization
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown, testthat, RcppML, BiocStyle
VignetteBuilder: knitr
URL: https://github.com/YMa-lab/CARDspa
BugReports: https://github.com/YMa-lab/CARDspa/issues
Config/pak/sysreqs: libabsl-dev cmake libfontconfig1-dev
        libfreetype6-dev libgdal-dev gdal-bin libgeos-dev make
        libmagick++-dev gsfonts libicu-dev libuv1-dev libssl-dev
        libproj-dev libsqlite3-dev libudunits2-dev libnode-dev
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:04:29 UTC
RemoteUrl: https://github.com/bioc/CARDspa
RemoteRef: RELEASE_3_23
RemoteSha: 67bc02b4fce8d9adef218d2e9a4b142eba0d294b
NeedsCompilation: yes
Packaged: 2026-04-29 18:41:13 UTC; root
Author: Ying Ma [aut],
  Jing Fu [cre]
Maintainer: Jing Fu <jing_fu@brown.edu>
Built: R 4.6.0; x86_64-w64-mingw32; 2026-04-29 18:54:34 UTC; windows
Archs: x64
