<h1 id="feature-detection"><a aria-hidden="true" class="anchor-heading icon-link" href="#feature-detection"></a>Feature Detection</h1>
<p>nf-core/metaboigniter is a bioinformatics pipeline that ...</p>
<p>This pipeline ingests raw mass spectrometry data in mzML format, typically in the form of peak lists and MS2 spectral data, for comprehensive metabolomics analysis. The key stages involve centroiding, feature detection, adduct detection, alignment, and linking, which progressively refine and align the data. The pipeline can also perform requantification to compensate for missing values and leverages MS2Query for compound identification based on MS2 data, outputting a comprehensive list of detected and potentially identified metabolites.</p>
<p><a href="https://github.com/nf-core/metaboigniter/tree/2.0.0">https://github.com/nf-core/metaboigniter/tree/2.0.0</a></p>

Feature Detection

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

