5_characterize_iModulons

Step 5: Characterize iModulons

This folder contains five Jupyter notebooks that outline the following characterization steps:

1. Creating a gene annotation table
2. Performing regulon, KEGG, and GO enrichments
3. Curating enrichments and iModulon thresholds
4. Searching for motifs
5. Creating an iModulonDB dashboard

To run these notebooks, you can either install Jupyter Notebook or install all requirements listed in the environment.yml file on the main page, or use a pre-existing docker container.

Running the docker container

1. Install Docker
2. Run the following code in terminal

docker run -p 8888:8888 avsastry/modulome-workflow:v1.0

3. Select the third link in terminal (starts with 127.0.0.1)
4. Navigate to the 5_characterize_iModulons folder and open the notebooks. Any changes made here will not be saved outside of the container.

Mounting local files in the Docker container

If you want to edit and save files in the docker container, replace the above command with the following:

docker run -p 8888:8888 -v <target-path>:/home/jovyan/work avsastry/modulome-workflow:v1.0

The above commands will mount the files in your local <target-path> to /home/jovyan/work in the Docker container. These files are editable, and changes made in the docker container will be reflected on your own machine. Only subfolders and files within <target-path> can be accessed by the container, so it is recommended to input the root folder of this repository as the <target-path>.

For more options, such as changing the default username, changing the port, or granting root access, see the Jupyter Docker Stacks Feature page

Eukaryotic functions

Plotting chromosomes and reading gff files for yeast are functions displayed in the eukaryotic_functions notebook. This notebook requires PyModulon 1.0.0 or later in order for functions to be installed correctly. See the pymodulon github for information on installing this version of the package.