AltAnalyze3 Documentation
=========================

Welcome to the AltAnalyze3 documentation!

AltAnalyze3 is an advanced Python3 workflow for long-read (LR) and short read analysis. Combine results across samples or technologies for supervised and unsupervised splicing/isoform analyses. See tutorials for examples.

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

   installation
   quickstart
   api_reference
   tutorials/long_read_analysis
   tutorials/differentials
   tutorials/splice_icgs

.. image:: ./images/AltAnalyze3.png
   :height: 500px
   :width: 737px
   :align: center
   :target: target
   
Getting Started
---------------

To begin using AltAnalyze3, follow the steps in the :doc:`installation` section. For a brief overview, visit the :doc:`quickstart` guide.

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

- Integrated long-read isoform analysis.
- Protein-level impacts of splicing and isoforms.
- Automated single-cell and differential analyses.
- Integration of bulk and single-cell data.
- Alternative promoter, retained intron and alternative polyadenylation regulation.

API Documentation
-----------------

For detailed descriptions of the available modules and their usage, see the :doc:`api_reference`.

Tutorials
---------

Our tutorials cover essential workflows, including:

- **Long Read Analysis**: :doc:`tutorials/long_read_analysis`
- **Short Read Analysis**: :doc:`tutorials/short_read_analysis`
- **Differential Analysis**: :doc:`tutorials/differentials`
- **Splice-ICGS Analysis**: :doc:`tutorials/splice_icgs`

Support
-------

If you encounter issues or need assistance, please visit our GitHub repository:  
https://github.com/SalomonisLab/altanalyze3