1.2.1

1.2.1

Bug Fixes

• Fixed an issue where {func}crested.pp.change_regions_width would not actually check for the chromsizes if a Genome was registered.

1.2.0

1.2.0

Features

• {func}crested.import_bigwigs now allows BED files with entries for chromsomes which are not in the BigWig.
• Better handling of bigwigs track in the backend and new bigwig track reading function {func}crested.utils.read_bigwig_region
• Overall support for stranded datasets while preserving support for non stranded datasets.
• DVC logging now available with tf backend
• New option to choose the starting sequences for motif implementation and ISE in enhancer design.
• {func}crested.tl.Crested.score_gene_locus now accepts an optional genome as input.
• output_activation now parameter for all models in zoo.
• {func}crested.utils.reverse_complement and {func}crested.utils.fetch_sequences now available.
• Spearman correlation metric implementation
• Pattern plotting QOL updates
• poisson losses implemented at {class}crested.tl.losses.PoissonLoss and {class}crested.tl.losses.PoissonMultinomialLoss
• {class}crested.Genome and {func}crested.register_genome for better handling of genome files.
• MSECosine loss now uses a multiplier parameter instead of standard multiplication

Tutorials

• Introductory notebook now fully reproducible

Bug Fixes

• {func}crested.tl.Crested.get_embeddings now correcly updates .varm if anndata is passed instead of .obsm.
• Tangermeme moved out of optional dependencies for tf vs torch breaking mismatches.
• Fixed calculation of contribution scores with torch backend when using incompatible numpy version.
• Fix incorrect None return in Crested.test()

Breaking Changes

• If providing the same project_name and run_name, the Crested class will now assume that you want to continue training from existing checkpoints.
• 'genome_file' argument name everywhere updated to 'genome'

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

1.0.0

Initial release