1.3.0

1.3.0

This is a big release wherein we introduce our model repository and do a functional refactoring of our tl.Crested class.

Features

• new crested.get_model function to fetch models from crested model repository
• new enformer and borzoi model options in the crested zoo, as well as scripts for converting weights to keras format.
• new cut site bigwigs option for mouse cortex dataset
• new crested model repository in the readthedocs with model descriptions.
• new pattern clustering plot pl.patterns.clustermap_with_pwm_logos that shows PWM logo plots below the heatmap.
• Extra parameters options in modisco calculations and plotting regarding allowed seqlets per cluster and top_n_regions selection.
• option to color lines in gene locus scoring plotting
• extra ylim option in crested.pl.bar.prediction
• gene locus scoring plotting improvements

Bugfixes

• importing bigwigs now correctly accounts for regions that were removed due to chromsizes

Notebooks

• Rewrote the tutorials to use the new functional API (WIP).
• Expanded on the enhancer design section

Functional Refactor of crested.tl.Crested(...) class

In this large refactor we're moving everything from the Crested class that does not use both a model and the AnnDatamodule out to a new _tools.py module where everything will be functional.
All the old functions remain in the Crested class for backward compatibility (for now) but will now raise a deprecation warning.

We're giving up a bit of clarity for ease of use by combining functions that do the same on different inputs into one single function.

Equivalent new functions

• tl.Crested.get_embeddings(...) ---> tl.extract_layer_embeddings(...)
• tl.Crested.predict(...) ---> tl.predict(...)
• tl.Crested.predict_regions(...) ---> tl.predict(...)
• tl.Crested.predict_sequence(...) ---> tl.predict(...)
• tl.Crested.score_gene_locus(...) ---> tl.score_gene_locus(...)
• tl.Crested.calculate_contribution_scores(...) ---> tl.contribution_scores(...)
• tl.Crested.calculate_contribution_scores_regions(...) ---> tl.contribution_scores(...)
• tl.Crested.calculate_contribution_scores_sequence(...) ---> tl.contribution_scores(...)
• tl.Crested.calculate_contribution_scores_enhancer_design(...) ---> tl.contribution_scores(...)
• tl.Crested.tfmodisco_calculate_and_save_contribution_scores_sequences ---> tl.contribution_scores_specific(...)
• tl.Crested.tfmodisco_calculate_and_save_contribution_scores ---> tl.contribution_scores(...)
• tl.Crested.enhancer_design_motif_implementation ---> tl.enhancer_design_motif_insertion
• tl.Crested.enhancer_design_in_silico_evolution ---> tl.enhancer_design_in_silico_evolution

New functions

Some utility functions were hidden inside the Crested class but required to be made explicit.

• utils.calculate_nucleotide_distribution (advised for enhancer design)
• utils.derive_intermediate_sequences (required for inspecting intermediate results from enhancer design)

New behaviour

• All functions that accept a model can now also accept lists of models, in which case the results will be averaged across models.
• All functions use a similar api, namely they expect some 'input' that can be converted to a one hot encoding (sequences, region names, anndatas with region names), but now the conversion happens behind the scenes so the user doesn't have to worry about this and we don't have a separate function per input format.

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