Robrecht Cannoodt

@lazappi Just to confirm, after what we discussed, do you agree with the following? * `AnnData()` will return an `InMemoryAnnData` (default) or an `HDF5AnnData` if the user really wants to....

> There is no way to provide additional arguments Good point, I hadn't considered that. > Something else Would you be ok with splitting it up into: ```r AnnData

I'm not sure what you mean by the reverse direction. Oh, you mean when we want to convert an AnnData to SCE or Seurat? We can call `adata$to_SingleCellExperiment()` and `adata$to_Seurat()`....

I'm going to port these changes to a different branch because there are too many conflicts by now (sorry about that!) In summary, I will: * Make sure HDF5AnnData and...

Can you merge the main branch into this PR?

Closing this PR for now

Good point. How about we release a version 0.1.0 once support for X, obs, var, obs_names, var_names and layers is implemented and unit tested for the HDF5AnnData, InMemoryAnnData, SeuratConverter and...

Can you show me the head of your dataset? You may want to run `Matrix::sparseMatrix(...)` to create a sparse matrix from your input data.

Thanks for the suggestion! I'm currently looking into it, I'll keep you posted :)

I think a good first step would be to add a documentation vignette for how to run SCORPIUS with a SingleCellExperiment. Would you be willing to create a format_sce.Rmd (similar...