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Welcome to TM-SmiRs!
===========
**TM‑SmiRs** is an end‑to‑end Python package that allows screening microRNA sequences for binding accessibility and secondary structure. 
Specifically, TM-SmiRs, a 𝐓oehold 𝐌ediated 𝐒trand displacement 𝗺𝗶cro𝐑NA 𝐬creening package, was built with the objective of providing 
a unified toolkit to select clinically relevant humnan microRNA targets with optimal properties for hybridisation. The package may be used for
both diagnostic and therapeutic contexts. 🍐🍐🍐


Key Features
------------------

- Thermodynamic analysis of input sequences
- Sequence level similarity metrics against a human and non-human RT-qPCR reference primer (hsa-miR-16-5p and cel-miR-39-3p respectively)
- Radar plots for intuitive visual overview of balanced features
- Projection of user-specified microRNAs into a precomputed PCA embeddings graph with all categorised human microRNAs
- Interactive plotly maps for exploring results visually

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Getting Started
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To get started with **TM-SmiRs** , refer to :ref:`Overview` for a summary of what the package entails.
:ref:`Installation` will then guide you further into pip installation instructions, and :ref:`Documentation` finally provides a full list of list of available commands.

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Credits
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If using this package for your research, please cite our paper:

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    @article{shortcode,
        title={TM-SmiRs: An end-to-end structural microRNA screening package evaluating strand availability},
        author={Inga Van den Bossche, Ines Silva, Chaewon Park, Adam Creamer, Molly},
        journal={Nucleic Acids Research},
        volume={vol},
        number={no},
        pages={pg-pg},
        year={2025},
        doi={doi}
    }

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And if you find *TM-SmiRs* useful give it a star on GitHub! 🌟

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   <a class="github-button" href="https://github.com/ilv18/TM-SmiRs" data-icon="octicon-star" data-show-count="true" aria-label="Star TM-SmiRs on GitHub">Star</a>
   <script async defer src="https://buttons.github.io/buttons.js"></script>

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   :caption: Quick start:
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   overview
   installation
   documentation/documentation


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   :caption: User Upload:
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   interface/index-interface
   interactive_notebook.ipynb

.. toctree::
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   :caption: Gallery:
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   examples/index-examples


.. toctree::
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   :caption: Links
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   GitHub repository <https://github.com/ilv18/TM-SmiRs>
   Paper <>