1.1.0

1.1.0

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