{"id":19197254,"url":"https://github.com/lolab-msm/magine","last_synced_at":"2025-05-09T00:39:37.338Z","repository":{"id":44866782,"uuid":"58402233","full_name":"LoLab-MSM/MAGINE","owner":"LoLab-MSM","description":"Mechanism of Action Generation involving Network Analysis","archived":false,"fork":false,"pushed_at":"2022-12-27T15:36:57.000Z","size":500610,"stargazers_count":9,"open_issues_count":4,"forks_count":5,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-05-09T00:39:23.621Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LoLab-MSM.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2016-05-09T19:26:13.000Z","updated_at":"2023-05-09T18:09:15.000Z","dependencies_parsed_at":"2023-01-31T05:31:00.888Z","dependency_job_id":null,"html_url":"https://github.com/LoLab-MSM/MAGINE","commit_stats":null,"previous_names":["lolab-vu/magine"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LoLab-MSM%2FMAGINE","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LoLab-MSM%2FMAGINE/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LoLab-MSM%2FMAGINE/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LoLab-MSM%2FMAGINE/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LoLab-MSM","download_url":"https://codeload.github.com/LoLab-MSM/MAGINE/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253171210,"owners_count":21865280,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-09T12:16:08.477Z","updated_at":"2025-05-09T00:39:37.313Z","avatar_url":"https://github.com/LoLab-MSM.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"=================================================================\nMAGINE : Mechanism of Action Generator involving Network Analysis\n=================================================================\n\n.. image:: https://app.codacy.com/project/badge/Grade/d5248a84f769428281e340bff1338963\n    :target: https://www.codacy.com/gh/LoLab-VU/MAGINE/dashboard?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=LoLab-VU/MAGINE\u0026amp;utm_campaign=Badge_Grade\n.. image:: https://github.com/LoLab-VU/MAGINE/actions/workflows/build.yml/badge.svg\n    :target: https://github.com/LoLab-VU/MAGINE/actions/workflows/build.yml\n.. image:: https://codecov.io/gh/LoLab-VU/MAGINE/branch/master/graph/badge.svg\n    :target: https://codecov.io/gh/LoLab-VU/MAGINE\n.. image:: https://readthedocs.org/projects/magine/badge/?version=latest\n   :target: https://magine.readthedocs.io/en/latest/?badge=latest\n   :alt: Documentation Status\n.. image:: https://mybinder.org/badge.svg\n    :target: https://mybinder.org/v2/gh/LoLab-VU/MAGINE/master\n.. image:: https://badges.gitter.im/LoLab-VU/MAGINE.svg\n   :target: https://gitter.im/LoLab-VU/MAGINE?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge\u0026utm_content=badge\n   :alt: Join the chat at https://gitter.im/LoLab-VU/MAGINE\n\nMAGINE is a framework for the analysis of quantitative multi-omics data.\nIt was designed to handle multi-sample (time points) and multi-omics\n(rnaseq, label-free proteomics, etc). Users are provided access to tools driven\naround their experimental data. Provides access to enrichment analysis, biological\nnetwork construction and various visualization methods.\n\n\nDocumentation\n=============\n\nThe manual is available online at http://magine.readthedocs.io.\n\n.. _Anaconda: https://www.anaconda.com/distribution/#download-section\n\nInstallation\n============\n\n1. Install Anaconda\n\n   Our recommended approach is to use Anaconda_, which is a\n   distribution of Python containing most of the numeric and scientific\n   software needed to get started. If you are a Mac or Linux user, have\n   used Python before and are comfortable using ``pip`` to install\n   software, you may want to skip this step and use your existing Python\n   installation.\n\n   Anaconda has a simple graphical installer which can be downloaded\n   from https://www.anaconda.com/distribution/#download-section - select\n   your operating system and download the **Python 3.7 version**. The\n   default installer options are usually appropriate.\n\n2. Open a terminal\n\n   We will install most packages with conda::\n\n      $ conda create -n magine_env python=3.7\n      $ conda activate magine_env\n      $ conda config --add channels conda-forge\n      $ conda install jinja2 statsmodels networkx graphviz\n      $ conda install -c marufr python-igraph\n\n   **Windows users:** Please download and install igraph and pycairo\n   using the wheel files provided by Christoph Gohlke, found at\n   https://www.lfd.uci.edu/~gohlke/ . Download and install via pip.\n\n3. Install MAGINE\n\n   The installation is very straightforward with ``pip`` - type the following in a terminal::\n\n      $ pip install magine\n\n4. Start Python and MAGINE\n\n   From the terminal or command prompt type ::\n\n      $ jupyter notebook\n\n   You will then be at the Python prompt. Type ``import magine`` to try\n   loading magine. If no error messages appear and the next Python\n   prompt appears, you have succeeded in installing magine!\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flolab-msm%2Fmagine","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flolab-msm%2Fmagine","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flolab-msm%2Fmagine/lists"}