.. scExtract documentation master file, created by
   sphinx-quickstart on Tue Oct 29 12:12:53 2024.

===============
scExtract
===============

.. toctree::
   :maxdepth: 2
   :caption: Contents:
   
   installation
   usage
   tutorials
   notebooks

Automated Single-Cell RNA-Seq Data Processing and Integration Framework
============================================================================

**scExtract** leverages Large Language Models for automated extraction, processing, annotation, and integration of published single-cell RNA sequencing data.

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

- **Article-based Processing**
    - Extract processing parameters from research papers
    - Support standard preprocessing workflows
    - Automated parameter selection

- **Cell Type Annotation**
    - LLM-assisted annotation process
    - Integration with common annotation tools
    - Support for marker gene validation

- **Dataset Integration**
    - Basic batch effect correction
    - Cross-dataset harmonization
    - Flexible integration options