Illustration from Scientific Research

Schematic of effective niche calculation: We aim to quantify the cell-type composition of each cells neighborhood. For each index cell, we calculate the pairwise kernel distance similarity between itself and each other cell in the sample. We use a Gaussian kernel with bandwidth . The effective niche for the index cell is a vector with dimension equal to the number of unique cell types in the sample where index i represents the sum of kernel similarities between the index cell and the cells of type i.

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