CARDspa

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see CARDspa.

Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

Bioconductor version: 3.21

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")):

Installation

To install this package, start R (version "4.5") 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 PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews SingleCell, Software, Spatial, Transcriptomics, Visualization

Version 1.0.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 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, RcppML, NMF, spatstat.random, gtools, SingleCellExperiment, SpatialExperiment

System Requirements

URL https://github.com/YMa-lab/CARDspa

Bug Reports https://github.com/YMa-lab/CARDspa/issues

Suggests knitr, rmarkdown, testthat, BiocStyle

Linking To Rcpp, RcppArmadillo

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CARDspa_1.0.0.tar.gz

Windows Binary (x86_64) CARDspa_1.0.0.zip (64-bit only)

macOS Binary (x86_64) CARDspa_1.0.0.tgz

macOS Binary (arm64) CARDspa_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/CARDspa

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CARDspa

Bioc Package Browser https://code.bioconductor.org/browse/CARDspa/

Package Short Url https://bioconductor.org/packages/CARDspa/

Package Downloads Report Download Stats