scvi-tools
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Deep probabilistic analysis of single-cell and spatial omics data
WIth the addition of AmortizedLDA, we would like to make incremental updates to improve the model. This issue will serve as the parent issue for a bunch of small features...
Our tests are a bit of a mess, we should figure out a more logical way to test everything.
https://pypi.org/project/towncrier/
It would be nice to alter the github workflow to test black, flake8 etc separately from pytest so a code styling issue doesn't halt the pytests.
Hello and so happy to see you use Pytorch-Lightning! :tada: Just wondering if you already heard about quite the new **Pytorch Lightning (PL) ecosystem CI** where we would like to...
https://www.biorxiv.org/content/10.1101/2020.12.26.424452v1
Hi, I am trying to integrate mostly paired scRNA and scATAC data following your MULTIVI tutorial. Creating the mvi anndata and setting up the model with ``` scvi.model.MULTIVI.setup_anndata(adata_mvi, batch_key='modality') ```...
We love scVI and use it all the time for batch-effect correction / dataset harmonization. As we scale to larger and larger datasets, we seem to have hit a wall...
Proposal to implement scHPF. 1. Code: https://github.com/simslab/scHPF 2. Paper: https://www.embopress.org/doi/full/10.15252/msb.20188557 Level of difficulty: Intermediate/advanced. Probably best to use Pyro for this one.