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Functional refactor#81

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LukasMahieu wants to merge 43 commits intomainaertslab/CREsted:mainfrom functional_refactoraertslab/CREsted:functional_refactorCopy head branch name to clipboard

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Commits on Nov 26, 2024

• init tools, move get_embeddings to tooling (with unit tests), input format detection

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• shape fix in docstring

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• move predict to tooling & unittests

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• allow multiple models as input to predict

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Commits on Nov 27, 2024

• score_gene_locus + unit tests in tooling ml and removed window_size

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• correctly use test fixtures

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• test units that ensure functionality is the same as before

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• contribution scores to tl ml + unit tests

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Commits on Nov 28, 2024

• specific contrib scores (for modisco) to tooling + unit tests

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Commits on Dec 10, 2024

• contribution scores specific

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Commits on Dec 11, 2024

• small docstring fix

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• merge from main

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• update all tests and tools to use new Genome

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• fix saving of contrib scores based on id

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• add repr and acgt distrib to genome

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Commits on Dec 12, 2024

• type int in genome.fetch

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• calculate gc distribution util function

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Commits on Dec 17, 2024

• Merge branch 'main' into functional_refactor

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• Merge branch 'functional_refactor' of https://github.com/aertslab/CREsted into functional_refactor

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• calculate nucleotide distributions in input

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Commits on Dec 19, 2024

• refactor enhancer_design and helper functions

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Commits on Jan 2, 2025

• start rewrite tutorial

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Commits on Jan 16, 2025

• use chr, start, end again instead of region name to match plotting func

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• merge main

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• start rewrite tutorial

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• start rewrite tutorial

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Commits on Jan 22, 2025

• start rewrite tutorial

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Commits on Jan 30, 2025

• update tutorial

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• Merge branch 'main' into functional_refactor

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• normalize acgt distribution to get rid of floating point errors

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Commits on Jan 31, 2025

• add enhancer_optimization functions and use target instead of target_idx

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• More extensive EnhancerOptimizer docs

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• rename motif implementation to motif insertion

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• update tests to match new function names

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• add util funciton derive_intermediate_sequences

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• rewrite tutorial to use functional api and add enhancer design

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• update docs index

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• minor docstring updates

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• minor docstring updates

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• add deprecation warnings to crested class

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• missing from future import

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Commits on Feb 4, 2025

• Merge branch 'main' into functional_refactor

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• notebooks updated

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