Features
- enhancer design plotting and calculation functions in the `crested.tl.Crested` object
- new module `crested.tl.modisco` with enhancer code analysis functionality
- new plots for enhancer code analysis in `crested.pl.patterns`
- new plot for sequence prediction in `crested.pl.bar`
- hidden utility functions now public in `crested.utils` (such as one hot encoding)
- CosineMSELog loss now default in peak_regression configs instead of CosineMSE
- tangermeme tomtom option in tfmodisco functions
- get_embeddings based on layer name in `crested.tl.Crested`
- `crested.utils.EnhancerOptimizer` utility function
- `crested.utils.permute_model` utility, useful for using with other toch packages
- `crested.utils.extract_bigwig_values_per_bp` utility
- improved correlation calculation speed in heatmaps
Tutorials
- introductory notebook is updated with new functionality
- new enhancer code analysis tutorial
Bug Fixes
- transfer Learning function now doesn't expect the dense block anymore
- bigwigs importing checks if it can open the file instead of looking for .bw extension
- no more ambiguous names in bed importing
- version requirement for modiscolite
- general pattern matching code bugfixes
Breaking Changes
- utility functions and logging moved to `crested.utils`
- tfmodisco functionality moved to `crested.tl.modisco`
Other
- general documentation fixes
- style checks now enforced on push
- both tf and torch backend tests on push