ChatziFISH

Source code used to analyse smFISH data in Chatzitheodoridou et al. 2024

System requirements

Windows 10 64 bit, macOS > 10

Installation

Typical installation time: 20 minutes

1. Install Anaconda or Miniconda for Python 3.9. IMPORTANT: For Windows make sure to choose the 64 bit version.
2. Open a terminal and navigate to ChatziFISH folder (this folder)
3. Update conda with conda update conda. Optionally, consider removing unused packages with the command conda clean --all
4. Update pip with python -m pip install --upgrade pip
5. Create a virtual environment with the command conda create -n chatzi python=3.9
6. Activate the environment with the command conda activate chatzi
7. Install all the dependencies with pip install -r requirements.txt