Once studies grow to 20+ tissues, it becomes unreasonable to fit all the data into memory at once. The world needs workflows to handle this.
There are a few categories of solutions:
- Some analyses can be run on a subset selected from across the tissues, e.g. a survey of the cell types or niches present.
- Run analyses tissue by tissue, e.g. performing cell typing in a consistent way one tissue at a time. (This might call on the results from the subset analysis.) Or, obtain some interesting summary statistic like DE results from each tissue, then report the results across tissues.
- Joint analyses of all tissues that load data in batches. E.g., with the right linear algebra, you compute PCs from the whole dataset while only loading one tissue at a time.
It's somewhat complex to set up all the above; I think analysts out there would benefit a lot from some vignettes.
Once studies grow to 20+ tissues, it becomes unreasonable to fit all the data into memory at once. The world needs workflows to handle this.
There are a few categories of solutions:
It's somewhat complex to set up all the above; I think analysts out there would benefit a lot from some vignettes.