# README: GRNet [<img src=”https://img.shields.io/badge/DOI-WIP-FAB70C?style=flat&logo=doi”>]() [<img src=”https://img.shields.io/badge/PMID-WIP-326599?style=flat&logo=pubmed”>]() [](https://grnet.readthedocs.io/en/latest/?badge=latest) [<img src=”https://img.shields.io/badge/Documentation-grnet.rtfd.io-8CA1AF?style=flat&logo=readthedocs”>](https://grnet.readthedocs.io/en/latest/) [<img src=”https://img.shields.io/badge/Code_Examples-Jupyter_Notebook-F37626?style=flat&logo=jupyter”>](https://grnet.readthedocs.io/en/latest/examples.html) [<img src=”https://img.shields.io/badge/GitHub-yo–aka–gene/grnet-181717?style=flat&logo=github”>](https://github.com/yo-aka-gene/grnet)

• This repository is also for analysis codes in $”Article;WIP”$

## Documentation <img src=”https://raw.githubusercontent.com/yo-aka-gene/grnet/main/docs/_static/title.PNG”>

• Documentation and example codes (jupyter notebooks) are available in [https://grnet.readthedocs.io/en/latest/index.html](https://grnet.readthedocs.io/en/latest/index.html)

## Installation This pkg is still a beta version. We will add this pkg to PyPI so that you will be able to install it via: ` pip install `

## Start Guide for Developers (& Researchers Interested in Reproducing Our Analysis) ### 1. Environment Preference - MacOS is preferred - Make sure you installed the following softwares:

• Homebrew (optional): [https://brew.sh/](https://brew.sh/)

• git: [https://formulae.brew.sh/formula/git](https://formulae.brew.sh/formula/git)

• Make: [https://formulae.brew.sh/formula/make](https://formulae.brew.sh/formula/make)

• poetry: [https://formulae.brew.sh/formula/poetry](https://formulae.brew.sh/formula/poetry)

• Docker Desktop: [https://formulae.brew.sh/cask/docker](https://formulae.brew.sh/cask/docker)

### 2. How to reproduce the virtual env - clone [this repository](https://github.com/yo-aka-gene/grnet) - activate the virtual env by runnning init.sh in grnet/grnet_sandbox directory. This shell script will automatically setup the virtual env and connect to it

` sh init.sh ` Note: Our docker container will occupy localhost:8000

• password for the JupyterLab server is jupyter

• install dependencies by calling the following inside the jupyter env

  ` sh lib.sh `

• you may need to install R dependencies for some codes in .ipynb files

  ` Rscript /home/jovyan/tools/set_renv.R `

### 3. Run codes - to reproduce all outputs at a time with a pipeline, run codes in /home/jovyan/code/experiment_execution.ipynb - If you are interested in taking a detailed look at each analysis, we have [online documentation](https://grnet.readthedocs.io/en/latest/index.html) and the same ipynb files are in /home/jovyan/docs/notebooks as well.