celldrl-ai 0.1.0

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:

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 Enviroment:

   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.

6. Open your jupyterlab book:

   jupyter lab
   

Tutorial

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