Workflow from Scientific Research

Schematic of niche-DE pipeline: To perform niche-DE, we first perform deconvolution/cell-type identification of our data. We then calculate the effective niche using a Gaussian kernel of bandwidth . We then apply the regression-based niche-DE model using the effective niche calculated in the previous step. If one desires, they can repeat this step for multiple bandwidths. Using the Cauchy combination test across the different kernels used, we can calculate a p -value for testing whether gene g is an (i,n) niche gene for all genes g and index-niche cell-type pairs.

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