pymodulon 0.2.0

Python package for analyzing and visualizing iModulons.

What is an iModulon?

To learn about iModulons, how they are computed, and what they can tell you, see our about page.

Installation

You can install PyModulon from PyPI using pip as follows:

pip install pymodulon

Alternatively, you can install using Conda:

conda install -c avsastry -c conda-forge pymodulon

We recommend installing through a conda environment:

conda create -n pymodulon -c conda-forge pymodulon
conda activate pymodulon

(Optional) Install other dependencies:

conda install -c anaconda graphviz
conda install -c bioconda meme blast

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.

Since PyModulon is currently under development, the recommended method to install PyModulon is to use the editable pip installation within a virtual environment or conda environment.

First initialize the conda environment:

conda create -n pymodulon-dev python=3.8
conda activate pymodulon-dev

(Optional) Install other dependencies:

conda install -c anaconda graphviz
conda install -c bioconda meme blast

Next, download the github repository:

git clone https://github.com/SBRG/pymodulon.git

Then install with pip using the -e flag:

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.