Workflow from Scientific Research

NicheCompass takes single-sample or multi-sample spatial omics data with cell-level or spot-level observations as input. Using the 2D coordinates, it constructs a spatial neighborhood graph (represented with a binary adjacency matrix), with each cell or spot representing a node. Each observation includes omics features (gene expression and optionally paired chromatin accessibility) and covariates to account for confounders (for example, sample).

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