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mchernigovskaya authored Nov 4, 2024
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Expand Up @@ -11,7 +11,7 @@ The LIgO manuscript showcases LIgO on two use cases. The following sections prov
2. :ref:`Manuscript use case 2: Limitations of conventional encoding schemes for repertoire-level binary classification when immune signals co-occur within the same AIR`


The following group of use cases is inspired by the manucript **"Revealing the hidden sequence distribution of epitope-specific TCR repertoires and its influence on machine learning model performance"** (`biorxiv <https://https://www.biorxiv.org/content/10.1101/2024.10.21.619364v1>`_). From these use cases you can learn how to define LIgO motifs inspired by VDJdb database, simulate epitope-specific TCRs based on these motifs, and inspect the simulated TCRs compared to experimental data.
The following group of use cases is inspired by the manucript **"Revealing the hidden sequence distribution of epitope-specific TCR repertoires and its influence on machine learning model performance"** (`biorxiv <https://www.biorxiv.org/content/10.1101/2024.10.21.619364v1>`_). From these use cases you can learn how to define LIgO motifs inspired by VDJdb database, simulate epitope-specific TCRs based on these motifs, and inspect the simulated TCRs compared to experimental data.

1. :ref:`Constructing LIgO motifs inspired by a database of TCR sequences with known antigen specificities`

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