API

import crested

• Datasets
  • 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.train_val_test_split
  • crested.pp.filter_regions_on_specificity
  • crested.pp.sort_and_filter_regions_on_specificity
  • crested.pp.normalize_peaks
  • crested.pp.change_regions_width
• Tools tl
  • crested.tl.Crested
  • crested.tl.TaskConfig
  • crested.tl.default_configs
  • crested.tl.predict
  • crested.tl.score_gene_locus
  • crested.tl.contribution_scores
  • crested.tl.contribution_scores_specific
  • crested.tl.extract_layer_embeddings
  • crested.tl.enhancer_design_in_silico_evolution
  • crested.tl.enhancer_design_motif_insertion
  • Data
  • Model Zoo
  • Losses
  • Metrics
  • Modisco
• Plotting: pl
  • crested.pl.render_plot
  • Patterns: Contribution scores and Modisco results
  • Bar plots
  • Distribution plots
  • Correlation heatmaps
  • Locus plots
  • Scatter plots
  • Violin plots
• Utils
  • crested.utils.EnhancerOptimizer
  • crested.utils.read_bigwig_region
  • crested.utils.hot_encoding_to_sequence
  • crested.utils.one_hot_encode_sequence
  • crested.utils.fetch_sequences
  • crested.utils.reverse_complement
  • crested.utils.permute_model
  • crested.utils.calculate_nucleotide_distribution
  • crested.utils.derive_intermediate_sequences
  • crested.utils.setup_logging