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0.4.8

Overview

  • Functional overview of the SDK
    • Sampling
      • sequences submodule (API)
      • targets submodule (API)
      • samplers submodule (API)
    • Training a model (API)
    • Evaluating a model (API)
    • Using a model to make predictions (API)
    • Visualizing model predictions (API)
    • The utilities submodule (API)
  • Help
  • Installation
    • Installing with Anaconda
      • Installing selene with pip:
    • Installing from source
    • Additional dependency for running the CLI
  • Tutorials
  • Selene CLI operations and outputs
    • Overview
    • Operations
    • General configurations
    • Model architecture
      • Expected input class and methods
      • Model architecture configuration
    • A note for the following sections
    • Train
      • Required parameters
      • Optional parameters
      • Additional notes
      • Expected outputs for training
    • Evaluate
      • Required parameters
      • Optional parameters
      • Additional notes
      • Expected outputs for evaluation
    • Analyze sequences
      • Required parameters
      • Optional parameters
      • Prediction on sequences
        • Parameters
      • Variant effect prediction
        • Parameters
        • Additional note
      • In silico mutagenesis
        • Parameters for a single sequence input
        • Parameters for FASTA file input:
    • Sampler configurations
      • Samplers used for training (and evaluation, optionally)
        • Random positions sampler
        • Intervals sampler
        • Multiple-file sampler
      • Important note
      • Samplers used for evaluation
        • BED file sampler
        • Matrix file sampler
    • Examples of full configuration files
      • Training (using intervals sampler)
        • Some notes
      • Evaluate (using matrix file sampler)
      • Some notes
      • Analyze sequences (variant effect prediction)
        • Some notes
  • FAQ and additional resources
    • Extending Selene
    • Exporting a Selene-trained model to Kipoi
    • Hyperparameter optimization

Packages

  • selene_sdk
    • TrainModel
    • EvaluateModel
  • selene_sdk.interpret
    • sequence_logo
    • heatmap
    • ISMResult
    • rescale_score_matrix
    • load_variant_abs_diff_scores
    • variant_diffs_scatter_plot
    • ordered_variants_and_indices
    • sort_standard_chrs
  • selene_sdk.predict
    • AnalyzeSequences
  • selene_sdk.samplers
    • Sampler
    • OnlineSampler
    • IntervalsSampler
    • RandomPositionsSampler
    • MultiFileSampler
  • selene_sdk.samplers.file_samplers
    • BedFileSampler
    • MatFileSampler
  • selene_sdk.sequences
    • Sequence
    • Genome
    • Proteome
    • sequence_to_encoding
    • encoding_to_sequence
    • get_reverse_encoding
  • selene_sdk.targets
    • Target
    • GenomicFeatures
  • selene_sdk.utils
    • NonStrandSpecific
    • PerformanceMetrics
    • initialize_logger
    • load_features_list
    • load_model_from_state_dict
    • get_indices_and_probabilities
    • load_path (for config.yml)
    • instantiate (configuration object)
    • initialize_model
    • parse_configs_and_run
    • execute (run Selene operations)
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