v0.1 release
This release introduces changes listed below:
Big changes to code:
- Updates for compatibility with scvi-tools>=0.16.0
- Deleting pymc3 code
- Revised tutorial (including per cell type expression prediction
- Amortised NN using AutoGuideMessenger and option to use hierarchical guide
Changes to defaults:
- Changing our default
detection_alpha
because within-slide tech effects seem to be more prevalent than their absence (detection_alpha=20) and recommend to run both detection_alpha=20 and detection_alpha=200 in the tutorial.
Changes to docs
- Template issue: bug (version, are you following scvi-tools tutorial)
- Template issue: usage question (version, are you following scvi-tools tutorial, which technology was used to generate reference data / spatial data, how many cell types, how many batches, how many genes, how many spatial locations)
- Update tutorial to match scvi-tools tutorial
- Update tutorial according to this feedback #65 (comment)
- Delete pymc3 tutorials from documentation website (reorder the rest to make it easier to understand that pymc3 should not be used)
- Fix documentation website for various classes including user-facing
Cell2location
class (automodule->autoclass) - Update readme - shorten what's possible
- Update readme - future work
- Update readme - add link to Nat Biotech paper
- Update acknowledgements
- Update copyright date
- Revise colab version of the notebook (less posterior samples)
- Add this line to tutorial: "The values are stored in adata.uns[f"mod_coloc_n_fact{n_fact}"] in a similar output format main cell2location results."