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> Those are very simple things, but I'm also curious how you can do some advanced operations like group by having, window functions, CTEs, aggregate functions that return JSONB structure (so you don't have to send duplicate data and avoid N+1 queries). How do you use PostGIS?

You don't! That is not what an ORM is for. Use SQL. Any decent ORM with allow you to integrate SQL.

Check out the Fluent (query builder) and Eloquent (ORM) from Laravel. They allow all the features you want.