Can Ergen
Can Ergen
Hi, you have to add protein_expression_obsm_key to setup_anndata when setting up the model to use the protein data. MultiVI can handle RNA+protein+ATAC and any combination of these. There is no...
Can you please run https://docs.scvi-tools.org/en/1.0.2/tutorials/notebooks/scarches_scvi_tools.html with adding categorical covariate key in addition to the batch key and by replacing batch_key with categorical covariate key and verify that the results are...
This seems to be a problem with your CUDA installation on a specific workstations. Actually torch can't initialize. Can you check that: `nvidia-smi` works within the command line and that...
Closed due to inactivity.
Agreed seems like lowly maintained. I am then also against keeping it optional and we should just highlight it in some tutorial. With RAPIDS UMAP the need is also much...
@ori-kron-wis Can you switch loom to anndata.io (https://anndata.readthedocs.io/en/latest/generated/anndata.io.read_loom.html)? I assume we then support numpy>2.0. We should for now make pyMDE optional and set an optional requirement to numpy
I assume loompy is a tutorial dependency? Let's get rid of loompy. I set up dvc yesterday with gdrive backend. We could switch all our tutorials to use our own...
@martinkim0 Was this one ready to merge or are things missing?
Adressed by #2960
Hi, thanks for the suggestion. We are currently looking into supporting MappedCollection from lamindb. However, AnnCollection works with setup_anndata while MappedCollection requires Custom Dataloaders. Do you used AnnCollection in disk-backed...