<h1 id="pathway-analysis"><a aria-hidden="true" class="anchor-heading icon-link" href="#pathway-analysis"></a>Pathway Analysis</h1>
<p>Looking for scripts and approaches to perform pathway analysis on plants/bacterial metabolomics dataset</p>
<h1 id="ressources"><a aria-hidden="true" class="anchor-heading icon-link" href="#ressources"></a>Ressources</h1>
<ul>
<li>A Systems Biology Workflow to Support the Diagnosis of Pyrimidine and Urea Cycle Disorders
<a href="https://github.com/BiGCAT-UM/IMD-PUPY">https://github.com/BiGCAT-UM/IMD-PUPY</a>
<a href="https://www.medrxiv.org/content/10.1101/2022.01.31.21265847v1">https://www.medrxiv.org/content/10.1101/2022.01.31.21265847v1</a></li>
</ul>
<ul>
<li>FELLA: an R package to enrich metabolomics data
<a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2487-5">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2487-5</a></li>
</ul>
<ul>
<li>
<p>Mummichog
<a href="https://shuzhao-li.github.io/mummichog.org/index.html">https://shuzhao-li.github.io/mummichog.org/index.html</a></p>
</li>
<li>
<p>Metaboverse
<a href="https://metaboverse.readthedocs.io/en/latest/">https://metaboverse.readthedocs.io/en/latest/</a> 😲😲😲😲</p>
</li>
</ul>
<p>TODO make a list of metabolomics analysis packages</p>
<h2 id="omu"><a aria-hidden="true" class="anchor-heading icon-link" href="#omu"></a>OMU</h2>
<p><a href="https://cran.r-project.org/web/packages/omu/vignettes/Omu_vignette.html">https://cran.r-project.org/web/packages/omu/vignettes/Omu_vignette.html</a></p>
<h2 id="secimtools-a-suite-of-metabolomics-data-analysis-tools"><a aria-hidden="true" class="anchor-heading icon-link" href="#secimtools-a-suite-of-metabolomics-data-analysis-tools"></a>SECIMTools: a suite of metabolomics data analysis tools</h2>
<p><a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2134-1">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2134-1</a></p>
<h2 id="a-practical-guide-to-metabolomics-software-development"><a aria-hidden="true" class="anchor-heading icon-link" href="#a-practical-guide-to-metabolomics-software-development"></a>A Practical Guide to Metabolomics Software Development</h2>
<p><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.0c03581">https://pubs.acs.org/doi/10.1021/acs.analchem.0c03581</a></p>
<h2 id="imap-a-web-server-for-metabolomics-data-integrative-analysis"><a aria-hidden="true" class="anchor-heading icon-link" href="#imap-a-web-server-for-metabolomics-data-integrative-analysis"></a>iMAP: A Web Server for Metabolomics Data Integrative Analysis</h2>
<p><a href="https://www.frontiersin.org/articles/10.3389/fchem.2021.659656/full">https://www.frontiersin.org/articles/10.3389/fchem.2021.659656/full</a></p>

A Practical Guide to Metabolomics Software Development

iMAP: A Web Server for Metabolomics Data Integrative Analysis

SECIMTools: a suite of metabolomics data analysis tools

Pathway Analysis

Concrete steps to access and contribute to the DBGI Dendron


![](/assets/images/allard-lab.jpg)

Welcome the the COMMONS Lab Open Dendron !

In the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.

For this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.

## What is this note

This note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.

## Tutorial

### Dendron. 

#### What is Dendron ?

> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.
> 
> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.

#### Where to get more info on Dendron ?

- You can get more information in the Dendron system at the official website www.dendron.so
- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.

#### Concrete steps to access and contribute to the DBGI Dendron

1. Install [VSCode](https://code.visualstudio.com/download)
2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace 
3. Clone the COMMONS Dendron repo

    In your terminal
    ```
    git clone https://github.com/commons-research/commons-dws-public.git
    ```
4. In VSCode open (File/Open) the cloned repository.
5. Voila ! You should now be in the COMMONS Lab Open Dendron.

Feel free to explore and contribute.
A first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]


## Questions, comments, suggestions ?

Feel free to contribute here https://github.com/orgs/commons-research/discussions

