Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

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Documentation for package ‘CARDspa’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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