Fig 3. The flowchart of the software.

Step 1 requires downloading and unzipping the scripts and data files. Step 2 consists of the installation of the necessary tools to run Omics Integrator. Step 3 describes how to prepare input files. Step 4 and 5 are designed for data collection and formatting for Garnet and Forest modules, respectively. At Step 6, configuration files are prepared where parameters are defined for Garnet and Forest separately. Garnet and Forest scripts are run at Step 7. If the initial data contains transcriptional data, then Garnet must be run before Forest. Otherwise Forest can be run independently. Detailed instructions of these steps are in the ‘Procedure’ section of the S1 Text.