<h1 id="qiime"><a aria-hidden="true" class="anchor-heading icon-link" href="#qiime"></a>Qiime</h1>
<h2 id="core-concepts"><a aria-hidden="true" class="anchor-heading icon-link" href="#core-concepts"></a>Core concepts</h2>
<p><a href="https://docs.qiime2.org/2020.8/concepts">https://docs.qiime2.org/2020.8/concepts</a></p>
<h2 id="semantic-types"><a aria-hidden="true" class="anchor-heading icon-link" href="#semantic-types"></a>Semantic types</h2>
<p><a href="https://docs.qiime2.org/2020.8/semantic-types/">https://docs.qiime2.org/2020.8/semantic-types/</a></p>
<h2 id="glossary"><a aria-hidden="true" class="anchor-heading icon-link" href="#glossary"></a>Glossary</h2>
<p><a href="https://docs.qiime2.org/2020.8/glossary/">https://docs.qiime2.org/2020.8/glossary/</a></p>
<h2 id="running-qiime"><a aria-hidden="true" class="anchor-heading icon-link" href="#running-qiime"></a>Running Qiime</h2>
<p><code>conda activate qiime2-2020.8</code></p>
<p><code>qiime</code></p>
<h2 id="lets-try-to-make-a-heatmap"><a aria-hidden="true" class="anchor-heading icon-link" href="#lets-try-to-make-a-heatmap"></a>lets try to make a heatmap</h2>
<p>qiime feature-table heatmap \
--i-table table-with-phyla.qza \
--o-visualization heatmap.qzv</p>
<h2 id="importing-and-exporting-tables"><a aria-hidden="true" class="anchor-heading icon-link" href="#importing-and-exporting-tables"></a>importing and exporting tables</h2>
<p>This passes by the BIOM format <a href="https://forum.qiime2.org/t/exporting-and-modifying-biom-tables-e-g-adding-taxonomy-annotations/3630">https://forum.qiime2.org/t/exporting-and-modifying-biom-tables-e-g-adding-taxonomy-annotations/3630</a></p>

Qiime

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

