Python package for analyzing and visualizing iModulons.
Project description
What is an iModulon?
To learn about iModulons, how they are computed, and what they can tell you, see our about page.
Installation
With Docker
The easiest way to get started with PyModulon is using the Docker container.
Install Docker
Open terminal and navigate to your work folder
Run the following commands to start a Jupyter Notebook server:
docker run -p 8888:8888 -v "${PWD}":/home/jovyan/work sbrg/pymodulonCopy the URL from terminal to connect to the Jupyter notebook
Navigate to the work folder, which has your current directory mounted.
To close the notebook, press Ctrl+C in terminal. All changes made to files in your current directory are saved to your local machine.
With Pip
You can install PyModulon from PyPI using pip as follows:
python -m pip install pymodulon
With Conda
Alternatively, you can install using Conda:
conda install -c conda-forge pymodulon
We recommend installing through a conda environment:
conda create -n pymodulon -c conda-forge pymodulon conda activate pymodulon
Optional Dependencies
Some features of PyModulon require additional dependencies. Follow the links below for installation instructions.
This step is not necessary if you use the Docker container.
Documentation
The documentation for PyModulon can be found here.
Development
If you would like to assist in development, please install pre-commit to ensure code style and consistency.
We recommend using an editable pip installation for development:
git clone https://github.com/SBRG/pymodulon.git cd pymodulon python -m pip install -e .
This method of installation will automatically update your package each time you pull from this repository.
To update your code, run the following from your local PyModulon folder:
git pull
Cite
Please cite the original E. coli iModulon paper: Sastry et al. Nature Communications. 2019.
If you use organism-specific datasets in your work, please cite these datasets:
Escherichia coli: Sastry et al. Nature Communications. 2019.
Bacillus subtilis: Rychel et al. Nature Communications. 2020.
Staphylococcus aureus: Poudel et al. PNAS. 2020.
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