scvi-tools
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Deep probabilistic analysis of single-cell and spatial omics data
Hello, I would like to know how MultiVI associates ATACseq peaks to genes. Does it associate it to TSS up/down some specific distance, or does it associate it to to...
When I am trying to analyze a large file created from an aggregate 10x multiom data with multiVI I receive an error when I run scvi.model.MULTIVI NOTE: This is a...
A subset of the hub tests fail due to array differences. Need to find a way to make these deterministic or increase the tolerance. These tests don't fail on cpu...
--------------------------------------------------------------------------- KeyError Traceback (most recent call last) Cell In[8], line 1 ----> 1 RNA_ATAC_model = scvi.model.MULTIVI.load(os.path.join(model_path, cur_best_model_path), adata=data_train) File ~/miniconda3/envs/py3/lib/python3.10/site-packages/scvi/model/base/_base_model.py:660, in BaseModelClass.load(cls, dir_path, adata, use_gpu, prefix, backup_url) 656 # Calling...
Hi! I have been trying to map data to scvi-integrated embeddings using scArches, and have noticed that for the two scVI-based reference models I have used, setting the `max_kl_weight` parameter...
Our current test suite that runs for every PR takes about 10-15 min. It doesn't need to be the case that all tests should be run for every change, though....
Ideas: - BatchNorm error with 1 obs in batch - NaNs during training - Difference between batch and categorical covariates #1613
- [x] Batch distributed sampler for efficient distributed sparse batching #2102 - [ ] Jax multi-device with `pmap` - [ ] Multi-device flag in pytest - [ ] Integrate with...
https://spatialdata.scverse.org/en/latest/ #1859