Getting Started
==============

Basic Usage
----------
This guide will help you quickly get started with GeneInsight for gene set analysis.

Input Files
^^^^^^^^^^
GeneInsight requires two input files:

1. **Query Gene Set**: A text file containing the genes of interest (one gene ID per line)
2. **Background Gene Set**: A text file containing a background set of genes for statistical comparison

Example Files
^^^^^^^^^^^
You can generate example files using the built-in utility:

.. code-block:: bash

   # Create an examples folder in your current directory
   geneinsight-examples
   
   # Or specify a custom destination
   geneinsight-examples --path /path/to/destination

Running Your First Analysis
-------------------------
Using the example files:

.. code-block:: bash

   geneinsight examples/sample.txt examples/sample_background.txt -o ./output

This will:

1. Process the query and background gene sets
2. Retrieve annotations from the STRING database
3. Perform topic modeling to identify biological themes
4. Apply statistical enrichment analysis
5. Generate an interactive HTML report

For detailed information about the output files and visualization, please refer to the :doc:`usage/output` documentation.

Next Steps
---------
* Try running GeneInsight with different parameter settings
* Explore the case studies in the Examples section
* Refer to the Usage documentation for advanced options