immuneML
2.1.2

Contents:

  • Quickstart
  • Installing immuneML
  • Tutorials
  • immuneML & Galaxy
  • YAML specification
  • Use case examples
    • Manuscript use case 1: Reproduction of a published study inside immuneML
    • Manuscript use case 2: Extending immuneML with a deep learning component for predicting antigen specificity of paired receptor data
    • Manuscript use case 3: Benchmarking ML methods on ground-truth synthetic data
    • Integration use case: post-analysis of sequences with Immcantation
    • Integration use case: post-analysis of sequences with immunarch
    • Integration use case: Performing analysis on immuneSIM-generated repertoires
  • Troubleshooting
  • Developer documentation
immuneML
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Use case examples

In the immuneML manuscript, we showcase immuneMLs functionalities based on three use cases. The following three sections describe how to reproduce these three use cases:

  1. Manuscript use case 1: Reproduction of a published study inside immuneML

  2. Manuscript use case 2: Extending immuneML with a deep learning component for predicting antigen specificity of paired receptor data

  3. Manuscript use case 3: Benchmarking ML methods on ground-truth synthetic data

To see how immuneML can be used in combination with other tools, see the following examples:

  1. Integration use case: post-analysis of sequences with Immcantation

  2. Integration use case: post-analysis of sequences with immunarch

  3. Integration use case: Performing analysis on immuneSIM-generated repertoires

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

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