Welcome to the BRAD-Examples repository! This repository provides a collection of example workflows and scripts to help users get started with BRAD—a chatbot and Python package designed to automate bioinformatics workflows and digital experiments.

These examples showcase how to leverage BRAD's features and capabilities in real-world scenarios. Whether you're new to BRAD or looking to expand your usage, this repository is a great starting point.

To use these examples, you'll need to install the BRAD Python package and set up the necessary dependencies. Detailed installation instructions can be found in the main BRAD repository.

• GUI Tutorial
  A simple tutorial for how to set up and use BRAD's Graphical User Interface.

• Hello World
  A simple "Hello, World!" example to help you understand the basics of using the BRAD chatbot.

• Search and Retrieval-Augmented Generation (RAG)
  Demonstrates how to use BRAD to scrape online data and integrate it into a Retrieval-Augmented Generation pipeline.

• Using the Scanpy Package with BRAD
  Explores how BRAD can streamline workflows involving Scanpy, including preprocessing and visualization of single-cell data.

• Biomarker Selection Pipeline
  Illustrates how BRAD can assist in selecting biomarkers from datasets using machine learning and bioinformatics tools.

Feel free to explore the examples and adapt them to your specific use cases. Happy experimenting with BRAD!