API

import crested

• Retrieve datasets & models
  • crested.get_dataset
  • crested.get_motif_db
  • crested.get_model
  • crested.Genome
  • crested.register_genome
• Input/Output
  • crested.import_bigwigs
  • crested.import_beds
• Preprocessing: pp
  • crested.pp.change_regions_width
  • crested.pp.filter_regions_on_specificity
  • crested.pp.normalize_peaks
  • crested.pp.sort_and_filter_regions_on_specificity
  • crested.pp.train_val_test_split
• Tools: tl
  • tl.data
  • tl.design
  • tl.losses
  • tl.metrics
  • tl.modisco
  • tl.zoo
  • crested.tl.Crested
  • crested.tl.TaskConfig
  • crested.tl.contribution_scores
  • crested.tl.contribution_scores_specific
  • crested.tl.default_configs
  • crested.tl.enhancer_design_in_silico_evolution
  • crested.tl.enhancer_design_motif_insertion
  • crested.tl.evaluate
  • crested.tl.extract_layer_embeddings
  • crested.tl.predict
  • crested.tl.score_gene_locus
• Plotting: pl
  • pl.corr
  • pl.design
  • pl.dist
  • pl.explain
  • pl.locus
  • pl.modisco
  • pl.qc
  • pl.region
  • crested.pl.create_plot
  • crested.pl.render_plot
• Utilities: utils
  • crested.utils.EnhancerOptimizer
  • crested.utils.calculate_nucleotide_distribution
  • crested.utils.derive_intermediate_sequences
  • crested.utils.fetch_sequences
  • crested.utils.flip_region_strand
  • crested.utils.hot_encoding_to_sequence
  • crested.utils.one_hot_encode_sequence
  • crested.utils.parse_region
  • crested.utils.read_bigwig_region
  • crested.utils.reverse_complement
  • crested.utils.setup_logging
• v2.0.0 renaming and deprecation