Package: CARDspa 0.99.5

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]

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CARDspa.pdf |CARDspa.html✨
CARDspa/json (API)
NEWS

# 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:

On BioConductor:CARDspa-0.99.5(bioc 3.21)

spatialsinglecelltranscriptomicsvisualizationopenblascppopenmp

4.48 score 3 scripts 9 exports 142 dependencies

Last updated 16 days agofrom:31984e0712. Checks:11 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 22 2025
R-4.5-win-x86_64OKFeb 22 2025
R-4.5-mac-x86_64OKFeb 22 2025
R-4.5-mac-aarch64OKFeb 22 2025
R-4.5-linux-x86_64OKFeb 22 2025
R-4.4-win-x86_64OKFeb 22 2025
R-4.4-mac-x86_64OKFeb 22 2025
R-4.4-mac-aarch64OKFeb 22 2025
R-4.3-win-x86_64OKFeb 22 2025
R-4.3-mac-x86_64OKFeb 22 2025
R-4.3-mac-aarch64OKFeb 22 2025

Exports:CARD_deconvolutionCARD_imputationCARD_refFreeCARD_scmappingCARD_visualize_CorCARD_visualize_geneCARD_visualize_pieCARD_visualize_propCARD_visualize_prop_2CT

Dependencies:abindaskpassBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocParallelbitbit64blobcachemclassclassIntcliclustercodacodetoolscolorspaceconcavemancpp11crayoncurlDBIdbplyrDelayedArraydeldirdigestdoParalleldotCall64dplyre1071fansifarverfastmapfieldsfilelockforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggcorrplotggforceggfunggplot2gluegridBasegtablegtoolshttrIRangesisobanditeratorsjsonliteKernSmoothlabelinglambda.rlatticelifecyclemagickmagrittrmapsMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmcmcMCMCpackmemoisemgcvmimemunsellnlmeNMFnnlsopensslpillarpkgconfigplogrplyrpolyclipproxypurrrquantregR6RANNRColorBrewerRcppRcppArmadilloRcppEigenRcppMLregistryreshape2rjsonrlangrngtoolsRSQLites2S4ArraysS4VectorsscalesscatterpiesfSingleCellExperimentsnowspspamSparseArraySparseMSpatialExperimentspatstat.dataspatstat.geomspatstat.randomspatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidyrtidyselecttweenrUCSC.utilsunitsutf8V8vctrsviridisLitewithrwkwrMiscXVectoryulab.utils

Example_Analysis

Ying Ma

Rendered fromExample_Analysis.Rmdusingknitr::rmarkdownon Feb 22 2025.

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

Readme and manuals

Help Manual

Help pageTopics
The function to assign the spatial location information for each single cellassign_sc_cords
Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics by CARDCARD_deconvolution
Construct an enhanced spatial expression map on the unmeasured tissue locationsCARD_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 correlationCARD_visualize_Cor
Visualize the spatial distribution of cell type proportionCARD_visualize_gene
Visualize the spatial distribution of cell type proportion in a geom scatterpie plotCARD_visualize_pie
Visualize the spatial distribution of cell type proportionCARD_visualize_prop
Visualize the spatial distribution of two cell type proportions on the same plotCARD_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 modelCARDfree
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 modelCARDref
Construct the mean gene expression basis matrix (B), this is the faster versioncreate_ref
Create the CARD objectcreateCARDfreeObject
Create the CARD objectcreateCARDObject
The function to sample the spatial location information for each single cellget_high_res_cords
The function to estimate the cell type composition signature for each single cell in the scRNaseq reference dataget_weight_for_cell
marker gene listmarkerList
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 locationsmvn_cv
Normalize the new spatial locations without changing the shape and relative positionsnorm_coords_train_test
Make new spatial locations on unmeasured tissue through grids.sample_grid_within
scRNA-seq count datasc_count
scRNAseq meta datasc_meta
Quality control of scRNA-seq count datasc_QC
Select Informative Genes used in the deconvolutionselect_info
Show method for the CARD classshow,CARD-method
Show method for the CARDfree classshow,CARDfree-method
Calculate the variance covariance matrix used in the imputation of the new grided locationsSigma
Spatial transcriptomics count dataspatial_count
Spatial location dataspatial_location