ImmunoPheno: a data-driven platform for the design and analysis of immunophenotyping experiments
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ImmunoPheno is a data-driven bioinformatics platform designed to facilitate the design and analysis of 
immunophenotyping experiments. It addresses the limitations of current cytometry
techniques by enabling researchers to design optimized antibody panels for specific cell populations 
and to more accurately identify and annotate cells in multiplexed antibody-based 
cytometry data. By leveraging single-cell proteotranscriptomic atlases (e.g., CITE-seq), ImmunoPheno enhances the phenotypic resolution,
annotation, accuracy, and reproducibility in immunophenotyping workflows.

Contents
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.. toctree::
   :maxdepth: 2
   :caption: OVERVIEW

   what-is-immunopheno

.. toctree::
   :maxdepth: 1
   :caption: TUTORIALS

   notebooks/Example_1
   notebooks/Example_2
   notebooks/Example_3
   notebooks/Example_4

.. toctree::
   :maxdepth: 1
   :caption: GALAXY USAGE

   galaxy_normalization
   galaxy_annotation
   galaxy_panel

.. toctree::
   :maxdepth: 2
   :caption: API

   normalization
   connect
   plots