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<!DOCTYPE html>
<html lang="en">
<head>
<title>Galaxy Europe</title>
<meta property="og:title" content="" />
<meta property="og:description" content="" />
<meta property="og:image" content="/assets/media/galaxy-eu-logo.512.png" />
<meta name="description" content="The European Galaxy Instance">
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<link rel="alternate" type="application/rss+xml" title="Galaxy Europe" href="/feed.xml">
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<div id="wrap">
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<div class="container" id="maincontainer">
<div class="home">
<p><img src="/assets/media/logo_single_cell.svg" alt="single cell Galaxy" width="25%" />
<img src="/assets/media/hca.png" alt="Human Cell Atlas" width="50%" /></p>
<h1 class="no_toc" id="welcome-to-the-single-cell-omics-lab">Welcome to the Single Cell Omics Lab!</h1>
<p>The Single Cell Omics and <a href="https://www.humancellatlas.org" target="_blank">The Human Cell Atlas</a> Galaxy enthusiasts have combined forces to bring you a single cell focused Galaxy Lab to make your analysis even easier. This resource is based on the Galaxy framework, which guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses independent of command-line knowledge.</p>
<p>This service is a joint project between different groups from the <a href="http://www.earlham.ac.uk" target="_blank">Earlham Institute</a>, the <a href="https://www.ebi.ac.uk/about/teams/gene-expression/" target="_blank">Gene Expression Team</a> at <a href="https://www.ebi.ac.uk/" target="_blank">EMBL-EBI</a>, the <a href="https://www.sanger.ac.uk/science/groups/teichmann-group" target="_blank">Teichmann Team</a> at the <a href="https://www.sanger.ac.uk/" target="_blank">Wellcome Sanger Institute</a>, <a href="https://gbcs.embl.de/" target="_blank">EMBL</a> the <a href="http://artbio.fr/" target="_blank">Sorbonne University</a>, <a href="https://www.petermac.org/" target="_blank">Peter MacCallum Cancer Centre</a> and the <a href="https://galaxyproject.eu/freiburg/" target="_blank">University of Freiburg</a>.</p>
<p>The server is part if the European Galaxy server and is maintained by the <a href="https://www.denbi.de/network/rna-bioinformatics-center-rbc" target="_blank">RNA Bioinformatics Center (RBC)</a> as part of <a href="https://www.denbi.de" target="_blank">de.NBI</a> and <a href="http://elixir-europe.org" target="_blank">ELIXIR</a>.</p>
<h1 class="no_toc" id="content">Content</h1>
<ol id="markdown-toc">
<li><a href="#get-started-with-single-cell" id="markdown-toc-get-started-with-single-cell">Get started with #single-cell</a></li>
<li><a href="#training" id="markdown-toc-training">Training</a></li>
<li><a href="#workflows" id="markdown-toc-workflows">Workflows</a></li>
<li><a href="#asking-for-help" id="markdown-toc-asking-for-help">Asking for help</a></li>
<li><a href="#asking-for-tools" id="markdown-toc-asking-for-tools">Asking for tools</a></li>
<li><a href="#join-the-single-cell-community-of-practice" id="markdown-toc-join-the-single-cell-community-of-practice">Join the Single Cell Community of Practice</a></li>
<li><a href="#contributors" id="markdown-toc-contributors">Contributors</a></li>
</ol>
<h1 id="get-started-with-single-cell">Get started with #single-cell</h1>
<p>Are you new to Galaxy, or returning after a long time, and looking for help to get started?</p>
<p>You may be interested in the following resources:</p>
<p><i class="fa fa-map" aria-hidden="true"></i> <a href="https://singlecell.usegalaxy.eu/tours/core.galaxy_ui">Guided tour</a> through Galaxy’s user interface.<br />
<i class="fa fa-road" aria-hidden="true"></i> <a href="https://training.galaxyproject.org/training-material/learning-pathways/intro_single_cell.html">Learning pathway for getting to grips with Galaxy and single cell</a><br />
<i class="fa fa-question-circle-o" aria-hidden="true"></i> <a href="https://help.galaxyproject.org/tag/scrna">Single cell help forum</a><br />
<i class="fa fa-comments-o" aria-hidden="true"></i> <a href="https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im">Single cell Galaxy user community chat room</a></p>
<h1 id="training">Training</h1>
<p>Want to learn even more about #single-cell analyses? You can check out our single cell training page within the wider Galaxy Training Network.</p>
<p><i class="fa fa-book" aria-hidden="true"></i> <a href="https://training.galaxyproject.org/training-material/topics/single-cell/">Single cell training material</a><br />
<i class="fa fa-mortar-board" aria-hidden="true"></i> <a href="https://galaxyproject.github.io/training-material/">the Galaxy Training Network</a></p>
<iframe src="https://training.galaxyproject.org/training-material/tags/single-cell/embed.html" height="600px" width="100%" class="gtn-embed" frameborder="0"></iframe>
<h1 id="workflows">Workflows</h1>
<p>In addition to our fantastic training materials, we encourage users to share their workflows!</p>
<p class="alert alert-success"><a href="https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_annotate.html">Tag your workflows</a> with <strong>#single-cell</strong> and share publicly with other users!</p>
<p>You can see shared workflows below.</p>
<iframe src="https://training.galaxyproject.org/training-material/workflows/embed.html?query=single-cell" height="600px" width="100%" class="gtn-embed" frameborder="0"></iframe>
<h1 id="asking-for-help">Asking for help</h1>
<p>Are you stuck? Galaxy is community driven, so we have a lot of resources to try and help you. In order, we suggest trying the following to get help!</p>
<ol>
<li><a href="https://help.galaxyproject.org/c/usegalaxy-eu-support/6">General help forum</a> or for single-cell specific questions, <a href="scrna">Single cell help forum</a></li>
<li><a href="https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im">Single cell Galaxy user community chat room</a></li>
<li><a href="https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im">Galaxy Training Community chat</a></li>
<li><a href="https://matrix.to/#/#usegalaxy-eu_Lobby:gitter.im">Usegalaxy.eu chat</a></li>
<li><a href="https://matrix.to/#/#galaxyproject_Lobby:gitter.im">Usegalaxy.org chat</a></li>
</ol>
<h1 id="asking-for-tools">Asking for tools</h1>
<p>Our Single Cell Community of Practice welcomes tool requests. We’re an open source, community-driven group, so we can’t guarantee everything, but we can certainly try to get the tools users need most into Galaxy! You can request tools at the following link:</p>
<p><a href="https://docs.google.com/spreadsheets/d/15hqgqA-RMDhXR-ylKhRF-Dab9Ij2arYSKiEVoPl2df4/edit?usp=sharing"><i class="fa fa-wrench" aria-hidden="true"></i> Tool Requests from Users</a></p>
<h1 id="join-the-single-cell-community-of-practice">Join the Single Cell Community of Practice</h1>
<p>Want to talk with trainers and developers on how to improve single cell analysis in Galaxy? Join the Community of Practice - we’re a nice bunch!</p>
<p><i class="fa fa-hand-o-right" aria-hidden="true"></i> Go to our <a href="https://galaxyproject.org/projects/singlecell/">Community of Practice site</a> to read more and join us!</p>
<!-- # Events and Workshops -->
<!-- We will be hosting a scRNA-seq workshop [this March](https://usegalaxy-eu.github.io/event/2020-01-20-GalaxyWS_scrna_FR/plain.html). Please register whilst spots are still open! -->
<h1 id="contributors">Contributors</h1>
<ul>
<li><a href="https://github.com/pcm32">Pablo Moreno</a></li>
<li><a href="https://github.com/mtekman">Mehmet Tekman</a></li>
<li><a href="https://github.com/pavanvidem">Pavankumar Videm</a></li>
<li><a href="https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/">Wendi Bacon</a></li>
<li><a href="https://github.com/kysrpex">José Domínguez</a></li>
<li><a href="https://github.com/astrovsky01">Alex Ostrovsky</a></li>
<li><a href="https://github.com/a-solovyev12">Andrey Solovyev</a></li>
<li><a href="https://github.com/bebatut">Bérénice Batut</a></li>
<li><a href="https://github.com/bgruening">Bjoern Gruening</a></li>
<li><a href="https://github.com/cartal">Carlos Talavera-Lopez</a></li>
<li><a href="https://github.com/cgirardot">Charles Girardot</a></li>
<li><a href="https://github.com/drosofff">Christophe Antoniewski</a></li>
<li><a href="https://github.com/blankenberg">Daniel Blankenberg</a></li>
<li><a href="https://github.com/fidelram">Fidel Ramirez</a></li>
<li><a href="https://github.com/ethering">Graham Etherington</a></li>
<li><a href="https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/">Helena Rasche</a></li>
<li><a href="https://twitter.com/irenepapatheodo">Irene Papatheodorou</a></li>
<li><a href="https://github.com/jxtx">James Taylor</a></li>
<li><a href="https://github.com/scholtalbers">Jelle Scholtalbers</a></li>
<li><a href="https://github.com/pinin4fjords">Jonathan Manning</a></li>
<li><a href="https://github.com/ktpolanski">Krzysztof Polanski</a></li>
<li><a href="https://github.com/bellenger-l">Lea Bellenger</a></li>
<li><a href="https://github.com/mblue9">Maria Doyle</a></li>
<li><a href="https://github.com/nh3">Ni Huang</a></li>
<li><a href="https://github.com/nsoranzo">Nicola Soranzo</a></li>
<li><a href="https://github.com/suhaibMo">Suhaib Mohammed</a></li>
</ul>
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Galaxy, it will be removed immediately, permanently.
An <a href="https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform" target="_blank">extended quota can be requested</a>
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<td>Any user data uploaded to our <a href="https://galaxyproject.eu/ftp/">FTP server</a> should be imported into Galaxy as soon
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<td>The Galaxy service complies with the EU General Data Protection Regulation
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User data on UseGalaxy.eu (i.e. datasets, histories) will be available as long
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<h4>GDPR Compliance</h4>
The Galaxy service complies with the EU General Data Protection Regulation
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<a href="https://usegalaxy.eu/terms/">Terms and Conditions</a>.
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