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  • Installation
  • Tutorials
    • Workflows
      • Introduction to CREsted with peak regression
      • Topic classification
      • Enhancer code analysis
      • Finetune Borzoi for scATAC peaks
    • Specific features
      • Custom models, losses, and metrics with CREsted
      • Model database fetching and inference
      • Multi-GPU training with TensorFlow
  • API
    • 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
        • crested.tl.data.AnnDataLoader
        • crested.tl.data.AnnDataModule
        • crested.tl.data.AnnDataset
        • crested.tl.data.SequenceLoader
      • tl.design
        • crested.tl.design.EnhancerOptimizer
        • crested.tl.design.derive_intermediate_sequences
        • crested.tl.design.in_silico_evolution
        • crested.tl.design.motif_insertion
      • tl.losses
        • crested.tl.losses.CosineMSELogLoss
        • crested.tl.losses.CosineMSELoss
        • crested.tl.losses.PoissonLoss
        • crested.tl.losses.PoissonMultinomialLoss
      • tl.metrics
        • crested.tl.metrics.ConcordanceCorrelationCoefficient
        • crested.tl.metrics.PearsonCorrelation
        • crested.tl.metrics.PearsonCorrelationLog
        • crested.tl.metrics.SpearmanCorrelationPerClass
        • crested.tl.metrics.ZeroPenaltyMetric
      • tl.modisco
        • crested.tl.modisco.calculate_mean_expression_per_cell_type
        • crested.tl.modisco.calculate_similarity_matrix
        • crested.tl.modisco.calculate_tomtom_similarity_per_pattern
        • crested.tl.modisco.create_pattern_matrix
        • crested.tl.modisco.create_pattern_tf_dict
        • crested.tl.modisco.create_tf_ct_matrix
        • crested.tl.modisco.find_pattern
        • crested.tl.modisco.find_pattern_matches
        • crested.tl.modisco.generate_html_paths
        • crested.tl.modisco.generate_nucleotide_sequences
        • crested.tl.modisco.get_pwms_from_modisco_file
        • crested.tl.modisco.match_h5_files_to_classes
        • crested.tl.modisco.pattern_similarity
        • crested.tl.modisco.process_patterns
        • crested.tl.modisco.read_motif_to_tf_file
        • crested.tl.modisco.tfmodisco
      • tl.zoo
        • tl.zoo.utils
        • crested.tl.zoo.basenji
        • crested.tl.zoo.borzoi
        • crested.tl.zoo.borzoi_prime
        • crested.tl.zoo.deeptopic_cnn
        • crested.tl.zoo.deeptopic_lstm
        • crested.tl.zoo.dilated_cnn
        • crested.tl.zoo.dilated_cnn_decoupled
        • crested.tl.zoo.enformer
        • crested.tl.zoo.simple_convnet
      • 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
        • crested.pl.corr.heatmap
        • crested.pl.corr.heatmap_self
        • crested.pl.corr.scatter
        • crested.pl.corr.violin
      • pl.design
        • crested.pl.design.step_contribution_scores
        • crested.pl.design.step_predictions
      • pl.dist
        • crested.pl.dist.histogram
      • pl.explain
        • crested.pl.explain.contribution_scores
      • pl.locus
        • crested.pl.locus.locus_scoring
        • crested.pl.locus.track
      • pl.modisco
        • crested.pl.modisco.class_instances
        • crested.pl.modisco.clustermap
        • crested.pl.modisco.clustermap_tf_motif
        • crested.pl.modisco.clustermap_tomtom_similarities
        • crested.pl.modisco.clustermap_with_pwm_logos
        • crested.pl.modisco.modisco_results
        • crested.pl.modisco.selected_instances
        • crested.pl.modisco.similarity_heatmap
        • crested.pl.modisco.tf_expression_per_cell_type
      • pl.qc
        • crested.pl.qc.filter_cutoff
        • crested.pl.qc.normalization_weights
        • crested.pl.qc.sort_and_filter_cutoff
      • pl.region
        • crested.pl.region.bar
        • crested.pl.region.scatter
      • 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.load_model
      • crested.utils.one_hot_encode_sequence
      • crested.utils.parse_region
      • crested.utils.permute_model
      • crested.utils.read_bigwig_region
      • crested.utils.reverse_complement
      • crested.utils.setup_logging
    • v1.7.0 renaming and deprecation
  • Models
    • ASAP
      • ASAP_CC
      • ASAP_SN
    • BICCN (Brain cortex)
      • DeepBICCN
      • DeepBICCN2
      • BorzoiBICCN
      • MouseCortexHydrop
    • Brain
      • DeepChickenBrain1
      • DeepChickenBrain2
      • DeepHumanBrain
      • DeepHumanCortex1
      • DeepHumanCortex2
      • DeepMouseBrain1
      • DeepMouseBrain2
      • DeepMouseBrain3
    • Cancer
      • DeepCCL
      • DeepGlioma
      • DeepMEL1
      • DeepMEL2
      • DeepMEL2 GABPA
    • Enformer/Borzoi
      • Borzoi
      • Borzoi Prime
      • Enformer
    • Fly
      • DeepFlyBrain
      • Embryo10x
      • EmbryoHydrop
    • Liver
      • DeepLiver Accessibility
      • DeepLiver Activity
      • DeepLiver Zonation
    • DeepPBMC
    • DeepZebraFish
  • Release notes
  • Contributing guide
  • References
  • How To Cite
  • License
  • .md

Tutorials

Tutorials#

  • Workflows
    • Introduction to CREsted with peak regression
    • Topic classification
    • Enhancer code analysis
    • Finetune Borzoi for scATAC peaks
  • Specific features
    • Custom models, losses, and metrics with CREsted
    • Model database fetching and inference
    • Multi-GPU training with TensorFlow

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Installation

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Workflows

By Aerts lab @ VIB.AI

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