Cell2location

This is the last pre-release before we introduce cell2location based on pyro and scvi-tools. The main purpose of this release is fixing package versions and dependencies for pymc3 implementation of models - which helps to provide docker image that reproducibly works with older models and older user interface (run_cell2location / run_regression / etc).

This pre-release includes 1) the model which can normalise within experiment variation in RNA detection sensitivity, 2) improvements to data visualisation, 3) major refactoring of how models are organised, 4) bug fixes (no critical bugs).

This pre-release includes updated tutorial notebooks, new Google Colab notebook, performance improvements (run_c2l and plot_spatial).

This pre-release adds gene selection by specificity to cell types, documentation and notebook improvements, some helpful error messages.

This pre-release contains pyro translation of cell2location, improved documentation and major refactoring of variable names incompatible with earlier versions.

Big update to cell2location documentation and renaming of model classes

- added tutorial about estimating reference signatures of cell types
- renamed model classes for readability
- pipelines can automatically select models (e.g. model with technical effects & multi-sample).