Confirm label transfer approach for neuroblastoma

[sjspielman]

For #1151, we had been planning to use scArches to perform label transfer to annotate NB samples. The goal of this issue to confirm this approach:

• Is there any reason to consider a different method? We know that scArches is reliably maintained, so there may not be, but it can't hurt to poke around a bit more in the latest-and-greatest literature.
• What computational resources are we looking at, and do we need GPU? How do resource this affect environment setup, if at all?
  • For example, so we have a sense if LSfR could accommodate GPU needs (if relevant)or would we need more resources?

[sjspielman]

Having spent some time reloading scArches and NBAtlas into my brain, the method indeed seems like the move. I'll look more into resource requirements coming up next, but first I want to note a couple initial items about NBAtlas that may be relevant to bear in mind:

• NBAtlas integrated with scVI, but they do not make their scVI model available. They do make Seurat objects with raw and normalized counts, cell/batch metadata (including cell types!), and the scVI latent representation available, but that representation isn't the same as the model itself.
• Either way, we'd want to use scANVI within the scArches framework, so we don't strictly need their scVI model. It might help us though to understand how it was created though:
  • Their code to build their scVI model is in this notebook
  • This appears to be their preprocessing data notebook to prepare each original dataset and export an anndata file for next steps, and that anndata file is slightly modified in this notebook. The output file from the second notebook matches the input file for the scVI notebook, so this seems right.

[sjspielman]

Noting that this is the NBAtlas notebook where they ran scANVI/scArches to incorporate in-house data, starting from their scVI model. May be useful to keep a hold of: https://github.com/VIBTOBIlab/NBAtlas_manuscript/blob/90bba8a6ca023f34ba5dffb7875e9ebdaac2bdd5/scArches_SCANVI_NBAtlas_v2_manuscript.ipynb#L226