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immuneML 3.0.2 documentation

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immuneML 3.0.2 documentation

Quickstart
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Installing immuneML
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YAML specification
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- How to specify an analysis with YAML
- YAML parameter details
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  - Definitions
  - Instructions
Tutorials
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- How to import data into immuneML
- How to generate a dataset with random sequences
- Dataset simulation with LIgO
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- How to train and assess a receptor or repertoire-level ML classifier
- How to apply previously trained ML models to a new dataset
- How to perform an exploratory data analysis
- How to find motifs associated with disease or antigen binding state
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immuneML & Galaxy
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Use case examples
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Troubleshooting
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Developer documentation
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- Information for new developers
- Set up immuneML for development
- How to add a new encoding
- How to add a new machine learning method
- How to add a new report
- How to add a new preprocessing
- immuneML data model
- immuneML execution flow
- immuneML
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  - immuneML package
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    - immuneML.IO package
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    - immuneML.analysis package
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    - immuneML.api package
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      - immuneML.api.aggregated_runs package
      - immuneML.api.galaxy package
    - immuneML.app package
    - immuneML.caching package
    - immuneML.data_model package
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      - immuneML.data_model.cell package
      - immuneML.data_model.dataset package
      - immuneML.data_model.encoded_data package
      - immuneML.data_model.receptor package
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        immuneML.data_model.receptor.receptor_sequence package
      - immuneML.data_model.repertoire package
    - immuneML.dev_util package
    - immuneML.dsl package
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    - immuneML.encodings package
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      - immuneML.encodings.abundance_encoding package
      - immuneML.encodings.atchley_kmer_encoding package
      - immuneML.encodings.deeprc package
      - immuneML.encodings.distance_encoding package
      - immuneML.encodings.evenness_profile package
      - immuneML.encodings.kmer_frequency package
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        immuneML.encodings.kmer_frequency.sequence_encoding package
      - immuneML.encodings.onehot package
      - immuneML.encodings.preprocessing package
      - immuneML.encodings.reference_encoding package
      - immuneML.encodings.word2vec package
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        immuneML.encodings.word2vec.model_creator package
    - immuneML.environment package
    - immuneML.hyperparameter_optimization package
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    - immuneML.ml_methods package
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      - immuneML.ml_methods.pytorch_implementations package
      - immuneML.ml_methods.util package
    - immuneML.ml_metrics package
    - immuneML.pairwise_repertoire_comparison package
    - immuneML.preprocessing package
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      - immuneML.preprocessing.filters package
    - immuneML.presentation package
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      - immuneML.presentation.html package
    - immuneML.reports package
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    - immuneML.simulation package
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    - immuneML.util package
    - immuneML.workflows package
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      - immuneML.workflows.instructions package
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        immuneML.workflows.instructions.dataset_generation package
        
        immuneML.workflows.instructions.exploratory_analysis package
        
        immuneML.workflows.instructions.ml_model_application package
        
        immuneML.workflows.instructions.subsampling package
      - immuneML.workflows.steps package
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        immuneML.workflows.steps.data_splitter package

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immuneML.data_model.encoded_data package¶

Submodules¶

immuneML.data_model.encoded_data.EncodedData module¶

Module contents¶

immuneML.data_model.receptor package

immuneML.data_model.dataset package

Copyright © 2021-2023, Milena Pavlovic, Lonneke Scheffer, Keshav Motwani, Victor Greiff, Geir Kjetil Sandve

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immuneML.data_model.encoded_data package