.. image:: ./images/flippr_long_logo.png
    :width: 800

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

FragPipe Limited-Proteolysis Processor (FLiPPR) is a modular, fast, and easy-to-use data processing tool for LiP-MS and LFQ-based experiments analyzed with FragPipe. It supports differential analysis and label-free quantification workflows and is designed to work with FragPipe output directories.

Quick start
-----------

For a minimal, runnable example and installation instructions, see the :doc:`quickstart` page.

Configuration
-------------

Global configuration values are available in the `rcParams` dictionary; see :doc:`how_to_use/rcParams` for details and examples.

API & examples
--------------

Browse the :doc:`api` reference for the public classes and helpers, and the :doc:`examples` page for common use cases.

Install
-------

Install FLiPPR from source into a recent Python environment (see `pyproject.toml` for the required Python version):

.. code-block:: bash

    uv sync

Install the published package into an existing environment:

.. code-block:: bash

    uv pip install flippr