Package: CARDspa 1.5.0

Jing Fu

CARDspa: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

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.

Authors:Ying Ma [aut], Jing Fu [cre]

CARDspa_1.5.0.tar.gz
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CARDspa_1.5.0.tgz(r-4.6-x86_64)CARDspa_1.5.0.tgz(r-4.6-arm64)CARDspa_1.5.0.tgz(r-4.5-x86_64)CARDspa_1.5.0.tgz(r-4.5-arm64)
CARDspa_1.5.0.tar.gz(r-4.7-arm64)CARDspa_1.5.0.tar.gz(r-4.7-x86_64)CARDspa_1.5.0.tar.gz(r-4.6-arm64)CARDspa_1.5.0.tar.gz(r-4.6-x86_64)
CARDspa_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CARDspa/json (API)

# Install 'CARDspa' in R:

install.packages('CARDspa', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yma-lab/cardspa/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

markerList - Marker gene list
sc_count - ScRNA-seq count data
sc_meta - ScRNAseq meta data
spatial_count - Spatial transcriptomics count data
spatial_location - Spatial location data

On BioConductor:CARDspa-1.5.0(bioc 3.24)CARDspa-1.4.0(bioc 3.23)

spatial singlecell transcriptomics visualization openblas cpp openmp

4.41 score 17 scripts 342 downloads 9 exports 136 dependencies

Last updated from:890e01d43c. Checks:1 NOTE, 13 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	258
linux-devel-arm64	OK	402
linux-devel-x86_64	OK	533
source / vignettes	OK	473
linux-release-arm64	OK	417
linux-release-x86_64	OK	679
macos-release-arm64	OK	438
macos-release-x86_64	OK	585
macos-oldrel-arm64	OK	421
macos-oldrel-x86_64	OK	772
windows-devel	OK	482
windows-release	OK	479
windows-oldrel	OK	461
wasm-release	OK	222

Exports:CARD_deconvolution CARD_imputation CARD_refFree CARD_scmapping CARD_visualize_Cor CARD_visualize_gene CARD_visualize_pie CARD_visualize_prop CARD_visualize_prop_2CT

Dependencies:abind askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocManager BiocParallel bit bit64 blob cachem class classInt cli cluster coda codetools colorspace concaveman cpp11 curl DBI dbplyr DelayedArray deldir digest doParallel dotCall64 dplyr e1071 farver fastmap fields filelock foreach formatR fs futile.logger futile.options generics GenomicRanges ggcorrplot ggforce ggfun ggplot2 glue gridBase gtable gtools httr2 IRanges isoband iterators jsonlite KernSmooth labeling lambda.r lattice lifecycle magick magrittr maps MASS Matrix MatrixGenerics MatrixModels matrixStats mcmc MCMCpack memoise NMF nnls openssl pillar pkgconfig plyr polyclip proxy purrr quantreg R6 RANN rappdirs RColorBrewer Rcpp RcppArmadillo registry reshape2 rjson rlang rngtools RSQLite s2 S4Arrays S4Vectors S7 scales scatterpie Seqinfo sf SingleCellExperiment snow sp spam SparseArray SparseM SpatialExperiment spatstat.data spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment survival sys systemfonts tensor tibble tidyr tidyselect tweenr units utf8 V8 vctrs viridisLite withr wk wrMisc XVector yulab.utils

Example_Analysis

Rendered fromExample_Analysis.Rmdusingknitr::rmarkdown

Last update: 2024-11-12
Started: 2024-06-26

Help page	Topics
The function to assign the spatial location information for each single cell	assign_sc_cords
Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics by CARD	CARD_deconvolution
Construct an enhanced spatial expression map on the unmeasured tissue locations	CARD_imputation
Extension of CARD into a reference-free version of deconvolution: CARDfree.	CARD_refFree
Extension of CARD into performing single cell Mapping from non-single cell spatial transcriptomics dataset.	CARD_scmapping
Visualize the cell type proportion correlation	CARD_visualize_Cor
Visualize the spatial distribution of cell type proportion	CARD_visualize_gene
Visualize the spatial distribution of cell type proportion in a geom scatterpie plot	CARD_visualize_pie
Visualize the spatial distribution of cell type proportion	CARD_visualize_prop
Visualize the spatial distribution of two cell type proportions on the same plot	CARD_visualize_prop_2CT
Each CARD object has a number of slots which store information. Key slots to access are listed below.	CARD-class
SpatialDeconv function based on Conditional Autoregressive model	CARDfree
Each CARDfree object has a number of slots which store information. Key slots to access are listed below.	CARDfree-class
SpatialDeconv function based on Conditional Autoregressive model	CARDref
Construct the mean gene expression basis matrix (B), this is the faster version	create_ref
Create the CARD object	createCARDfreeObject
Create the CARD object	createCARDObject
The function to sample the spatial location information for each single cell	get_high_res_cords
The function to estimate the cell type composition signature for each single cell in the scRNaseq reference data	get_weight_for_cell
marker gene list	markerList
Imputation and Construction of High-Resolution Spatial Maps for Cell Type Composition and Gene Expression by the spatial correlation structure between original spatial locations and new grided spatial locations	mvn_cv
Normalize the new spatial locations without changing the shape and relative positions	norm_coords_train_test
Make new spatial locations on unmeasured tissue through grids.	sample_grid_within
scRNA-seq count data	sc_count
scRNAseq meta data	sc_meta
Quality control of scRNA-seq count data	sc_QC
Select Informative Genes used in the deconvolution	select_info
Show method for the CARD class	show,CARD-method
Show method for the CARDfree class	show,CARDfree-method
Calculate the variance covariance matrix used in the imputation of the new grided locations	Sigma
Spatial transcriptomics count data	spatial_count
Spatial location data	spatial_location

Package: CARDspa 1.5.0

CARDspa: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

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