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scider is an user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for several downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.

hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.

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.