scvi-tools
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Deep probabilistic analysis of single-cell and spatial omics data
See [this](https://github.com/scverse/scvi-tools/pull/1812) PR for more context - [x] Account for data/model prefixes -> we chose not to do this to keep naming cohesive across the board (+ given that we...
**Is your feature request related to a problem? Please describe.** I want to develop a new model with Pytorch Geometric which is a GNN library based on Pytorch. I hope...
Hi, I see that `use_observed_lib_size=False` fails with NaN for some datasets. I would like to use `use_observed_lib_size=False` to estimate the technical normalisation effect per cell - which does not necessarily...
One thing we may need to consider is a util to patch loading old saves of multivi models if we remove setup anndata
Good day! I want to use `MultiVI` to integrate scRNA, scATAC and multiome (RNA+ATAC). I saw in the tutorial you read the files directly form the cellranger output directory, however,...
I'd like to be able to use SCANVI for clustering – i.e. to learn this generative model in a purely unsupervised setting in which I do not yet have any...
Is anyone currently working on implementing NSF? It's a nice probabilistic method designed with spatial transcriptomics in mind. https://www.nature.com/articles/s41592-022-01687-w It'd be nice to work with this here, within `scvi-tools`. The...
Create a separate method to detect observed sites and apply it everywhere necessary to automatically exclude observed sites. Fixes #1801
- [x] Verify that all parameters are being initialized equivalently, alter the ones used here if needed - [x] Add more content to the tutorial that reproduces their results, allowing...
Because of this line summary stats can be overwritten if two fields use the same name. Summary stats should be a dict with keys being the unique registry keys of...