celldrl-ai 0.1.1

AI Agent which reconstructs Intermediate paths from single-cell genomics data

Cell-DRL: AI agent reconstructs Intermediate paths from single-cell genomics data

Cell-DRL is a deep reinforcement learning agent capable of reconstructing intermediate cellular states in health, disease, and regenerative processes. Cell-DRL's cellular state reconstruction is based on defining initial and target cellular states of interest from single-cell RNA-seq data.

Installation

To set up Cell-DRL on your machine, follow these steps:

System Dependencies

Before installing the Python package, install the required system libraries:

sudo apt-get update
sudo apt-get install libsdl2-dev libsdl2-image-dev libsdl2-mixer-dev libsdl2-ttf-dev cmake

On macOS:

brew install sdl2 sdl2_image sdl2_mixer sdl2_ttf cmake

Python Installation

1. Download the package files:

   • Option 1: Using Git

     git clone https://gitlab.com/ama.bioinfo/cell-drl.git
     

   • Option 2: Downloading a ZIP file If you prefer not to use Git, you can download a ZIP file of the repository.

2. Open your Terminal:

   • On Windows, you can use Command Prompt or PowerShell.
   • On macOS or Linux, you can use the Terminal.

3. Navigate to the project directory:

   cd /path/to/your_project/celldrl_Dir/
   

4. Install New Conda Environment:

   conda create -n CellDRL_Env python=3.9
   conda activate CellDRL_Env 
   

5. Install the required dependencies:

   pip install -r requirements.txt
   

   This command will automatically install all the necessary packages listed in the requirements.txt file. The cmake dependency is now included in the build system, so it will be installed automatically.

6. Open your jupyterlab book:

   jupyter lab
   

Tutorial

Please open the tutorial folder to start running Cell-DRL agent jupyter notebook.