CARDspa
This is the released version of CARDspa; for the devel version, see CARDspa.
Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics
Bioconductor version: Release (3.23)
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("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.
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 | |
| LICENSE | Text |
Details
| biocViews | SingleCell, Software, Spatial, Transcriptomics, Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL-3 + file LICENSE |
| 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 |
| System Requirements | |
| URL | https://github.com/YMa-lab/CARDspa |
| Bug Reports | https://github.com/YMa-lab/CARDspa/issues |
See More
| Suggests | knitr, rmarkdown, testthat, RcppML, BiocStyle |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow 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 (64-bit only) |
| macOS Binary (big-sur-x86_64) | CARDspa_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | 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 Short Url | https://bioconductor.org/packages/CARDspa/ |
| Package Downloads Report | Download Stats |