Basic Examples
==============

This page provides basic examples of using GeneInsight for gene set analysis.

Example 1: Human Gene Set Analysis
--------------------------------

This example demonstrates the basic workflow for analyzing a human gene set.

Input Preparation
^^^^^^^^^^^^^^^

Save your gene list in a text file with one gene per line:

.. code-block:: text
    :caption: genes_of_interest.txt

    BRCA1
    BRCA2
    TP53
    ATM
    CHEK2
    PALB2
    RAD51
    BARD1

Similarly, prepare a background gene list:

.. code-block:: text
    :caption: background_genes.txt

    # This file contains a larger set of genes for statistical comparison
    # Format: one gene per line
    BRCA1
    BRCA2
    TP53
    ATM
    CHEK2
    PALB2
    RAD51
    BARD1
    # ...many more genes...

Running the Analysis
^^^^^^^^^^^^^^^^^

Execute GeneInsight with default parameters:

.. code-block:: bash

    geneinsight genes_of_interest.txt background_genes.txt -o ./dna_repair_analysis

This will:

1. Retrieve functional annotations from the STRING database
2. Perform topic modeling to identify biological themes
3. Apply statistical validation through hypergeometric testing
4. Generate an interactive HTML report

Exploring the Results
^^^^^^^^^^^^^^^^^

Navigate to the output directory and open the HTML report:

.. code-block:: bash

    cd dna_repair_analysis
    # Open unzip sphinx_build.zip and open index.html in your browser