.. TiRank documentation master file

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TiRank prioritizes phenotypic niches in tumor microenvironment for clinical biomarker discovery
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.. image:: _static/TiRank_white.png
   :width: 50%
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   :alt: TiRank Logo

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  :target: https://pypi.org/project/TiRank/
  :alt: PyPI
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  :target: https://anaconda.org/bioconda/tirank
  :alt: Bioconda
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.18275554.svg
  :target: https://doi.org/10.5281/zenodo.18275554
  :alt: Zenodo DOI
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  :target: https://github.com/LenisLin/TiRank/blob/main/LICENSE
  :alt: License
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  :alt: Documentation Status

TiRank is a toolkit designed to integrate and analyze RNA-seq and single-cell RNA-seq (scRNA-seq) data.
By combining spatial transcriptomics or scRNA-seq data with bulk RNA sequencing data, TiRank enables
phenotype-associated region/cluster discovery. The toolkit supports survival analysis (Cox),
classification, and regression.

.. image:: _static/FigS1.png
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   :align: center
   :alt: TiRank Workflow

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.. toctree::
   :maxdepth: 2
   :caption: Getting Started

   installation
   snakemake_workflow
   model_input

.. toctree::
   :maxdepth: 2
   :caption: CLI Tutorials

   tutorial_st_survival
   tutorial_sc_classification

.. toctree::
   :maxdepth: 2
   :caption: GUI Tutorial

   tutorial_web

.. toctree::
   :maxdepth: 1
   :caption: Features Document

   result_interpretation
   hyperparameters

.. toctree::
   :maxdepth: 1
   :caption: API Reference

   api

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Citing & Support
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For support, please use the GitHub Issues page: https://github.com/LenisLin/TiRank/issues

License
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TiRank is distributed under the MIT License.