Skip to content

v0.1 release

Compare
Choose a tag to compare
@vitkl vitkl released this 18 May 00:28
· 72 commits to master since this 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."