Niche universe

Every niche code from every dataset Nicheverse has modeled, placed in one shared space. Each point is one niche code of one dataset (3,748 niches from 129 datasets and 50.9 million cells across ten platforms), positioned by the correlation of its pseudobulk expression profile with every other niche over the genes their panels share, and grouped into 21 meta niches by Leiden clustering of the shared nearest neighbor graph. Scroll to zoom, drag to pan, click a point to see a spatial thumbnail of that niche in its tissue (cells of the niche in color over the rest of the section), hover a point for its dataset, platform, tissue, cell count, spatial coherence and top marker genes, use the menu to recolor by meta niche, platform, species, organ system or disease class, click a legend entry to isolate it, and type in the search box to highlight niches whose dataset or markers match.

The underlying table with one row per niche is served alongside the page as _static/niche_universe/niche_universe_points.json.