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Advanced gapped kmer, IC-based motif centering #63

Merged
merged 21 commits into from
Aug 26, 2020
Merged

Advanced gapped kmer, IC-based motif centering #63

merged 21 commits into from
Aug 26, 2020

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AvantiShri
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@AvantiShri AvantiShri commented Aug 26, 2020

Implementation for advanced gapped kmer embeddings, IC-based motif centering in the "expand-trim-expand" postprocessing steps, some other minor fixes/features (including ability to supply custom per-pos contrib score tracks).

To use advanced gapped kmer embeddings, supply seqlet_embedding.advanced_gapped_kmer.AdvancedGappedKmerEmbedderFactory() as the embedder_factory argument in tfmodisco_workflow.seqlets_to_patterns.TfModiscoSeqletsToPatternsFactory (which is in turn supplied as the seqlets_to_patterns_factory argument of tfmodisco_workflow.workflow.TfModiscoWorkflow)

@AvantiShri AvantiShri merged commit 8eb12ba into master Aug 26, 2020
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