scvi-tools
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Deep probabilistic analysis of single-cell and spatial omics data
- Take as input the release tag - Run PyPI publishing workflow - Build Docker images on success
Hi! I am unable to retrieve region factors with `model.get_region_factors()` for PoissonVI models (one trained on my own dataset, another trained on a subset of the tutorial PBMC data). The...
Closes https://github.com/scverse/scvi-tools/issues/2383
Here's an example code snippet for how this works with SCVI: ``` import scvi from scvi.autotune import ModelTuner from scvi.train._scib_callback import ScibCallback adata = scvi.data.synthetic_iid() model_cls = scvi.model.SCVI model_cls.setup_anndata(adata, batch_key="batch",...
When training the gimVI model, I am running into a ValueError in the first epoch for some datasets and not others. In all cases, the inputs are AnnData objects with...
Right now we split the data randomly be a user specified proportion. We should provide api access to allow any custom splits. A workaround right now is to train on...
**Is your feature request related to a problem? Please describe.** To make scvitools utilize gpus, Jax, cudatoolkit and torch all have to be installed without conflicts. **Describe the solution you'd...
We were considering adding cycle-consistency loss and VampPrior as described in [Integrating single-cell RNA-seq datasets with substantial batch effects | bioRxiv](https://www.biorxiv.org/content/10.1101/2023.11.03.565463v1)) to scvi-tools package, preferably directly into scVI. The current...