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| 32 | + <div class="home"> |
| 33 | + |
| 34 | + |
| 35 | + |
| 36 | + |
| 37 | + |
| 38 | + |
| 39 | + |
| 40 | + <p><img src="/assets/media/logo_single_cell.svg" alt="single cell Galaxy" width="25%" /> |
| 41 | +<img src="/assets/media/hca.png" alt="Human Cell Atlas" width="50%" /></p> |
| 42 | + |
| 43 | +<h1 class="no_toc" id="welcome-to-the-ghana-galaxy-instance">Welcome to the Ghana Galaxy Instance!</h1> |
| 44 | + |
| 45 | +<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. |
| 46 | +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> |
| 47 | + |
| 48 | +<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 |
| 49 | +<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> |
| 50 | + |
| 51 | +<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 |
| 52 | +<a href="https://www.denbi.de" target="_blank">de.NBI</a> and <a href="http://elixir-europe.org" target="_blank">ELIXIR</a>.</p> |
| 53 | + |
| 54 | +<h1 class="no_toc" id="content">Content</h1> |
| 55 | + |
| 56 | +<ol id="markdown-toc"> |
| 57 | + <li><a href="#get-started-with-single-cell" id="markdown-toc-get-started-with-single-cell">Get started with #single-cell</a></li> |
| 58 | + <li><a href="#training" id="markdown-toc-training">Training</a></li> |
| 59 | + <li><a href="#workflows" id="markdown-toc-workflows">Workflows</a></li> |
| 60 | + <li><a href="#asking-for-help" id="markdown-toc-asking-for-help">Asking for help</a></li> |
| 61 | + <li><a href="#asking-for-tools" id="markdown-toc-asking-for-tools">Asking for tools</a></li> |
| 62 | + <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> |
| 63 | + <li><a href="#contributors" id="markdown-toc-contributors">Contributors</a></li> |
| 64 | +</ol> |
| 65 | + |
| 66 | +<h1 id="get-started-with-single-cell">Get started with #single-cell</h1> |
| 67 | + |
| 68 | +<p>Are you new to Galaxy, or returning after a long time, and looking for help to get started?</p> |
| 69 | + |
| 70 | +<p>You may be interested in the following resources:</p> |
| 71 | + |
| 72 | +<p><i class="fa fa-map" aria-hidden="true"></i> <a href="https://ghana.usegalaxy.eu/tours/core.galaxy_ui">Guided tour</a> through Galaxy’s user interface.<br /> |
| 73 | +<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 /> |
| 74 | +<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 /> |
| 75 | +<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> |
| 76 | + |
| 77 | +<h1 id="training">Training</h1> |
| 78 | + |
| 79 | +<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> |
| 80 | + |
| 81 | +<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 /> |
| 82 | +<i class="fa fa-mortar-board" aria-hidden="true"></i> <a href="https://galaxyproject.github.io/training-material/">the Galaxy Training Network</a></p> |
| 83 | + |
| 84 | +<iframe src="https://training.galaxyproject.org/training-material/tags/single-cell/embed.html" height="600px" width="100%" class="gtn-embed" frameborder="0"></iframe> |
| 85 | + |
| 86 | +<h1 id="workflows">Workflows</h1> |
| 87 | + |
| 88 | +<p>In addition to our fantastic training materials, we encourage users to share their workflows!</p> |
| 89 | + |
| 90 | +<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> |
| 91 | + |
| 92 | +<p>You can see shared workflows below.</p> |
| 93 | + |
| 94 | +<iframe src="https://training.galaxyproject.org/training-material/workflows/embed.html?query=single-cell" height="600px" width="100%" class="gtn-embed" frameborder="0"></iframe> |
| 95 | + |
| 96 | +<h1 id="asking-for-help">Asking for help</h1> |
| 97 | +<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> |
| 98 | +<ol> |
| 99 | + <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> |
| 100 | + <li><a href="https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im">Single cell Galaxy user community chat room</a></li> |
| 101 | + <li><a href="https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im">Galaxy Training Community chat</a></li> |
| 102 | + <li><a href="https://matrix.to/#/#usegalaxy-eu_Lobby:gitter.im">Usegalaxy.eu chat</a></li> |
| 103 | + <li><a href="https://matrix.to/#/#galaxyproject_Lobby:gitter.im">Usegalaxy.org chat</a></li> |
| 104 | +</ol> |
| 105 | + |
| 106 | +<h1 id="asking-for-tools">Asking for tools</h1> |
| 107 | +<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> |
| 108 | + |
| 109 | +<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> |
| 110 | + |
| 111 | +<h1 id="join-the-single-cell-community-of-practice">Join the Single Cell Community of Practice</h1> |
| 112 | +<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> |
| 113 | + |
| 114 | +<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> |
| 115 | + |
| 116 | +<!-- # Events and Workshops --> |
| 117 | + |
| 118 | +<!-- 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! --> |
| 119 | + |
| 120 | +<h1 id="contributors">Contributors</h1> |
| 121 | + |
| 122 | +<ul> |
| 123 | + <li><a href="https://github.com/pavanvidem">Pavankumar Videm</a></li> |
| 124 | + <li><a href="https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/">Wendi Bacon</a></li> |
| 125 | + <li><a href="https://github.com/kysrpex">José Domínguez</a></li> |
| 126 | + <li><a href="https://github.com/astrovsky01">Alex Ostrovsky</a></li> |
| 127 | + <li><a href="https://github.com/a-solovyev12">Andrey Solovyev</a></li> |
| 128 | + <li><a href="https://github.com/bebatut">Bérénice Batut</a></li> |
| 129 | + <li><a href="https://github.com/bgruening">Bjoern Gruening</a></li> |
| 130 | + <li><a href="https://github.com/nsoranzo">Nicola Soranzo</a></li> |
| 131 | + <li><a href="https://github.com/suhaibMo">Suhaib Mohammed</a></li> |
| 132 | +</ul> |
| 133 | + |
| 134 | + |
| 135 | +<h2>Our Data Policy</h2> |
| 136 | + |
| 137 | + |
| 138 | + <table class="table table-striped"> |
| 139 | + <thead> |
| 140 | + <tr> |
| 141 | + <th>Registered Users</th><th>Unregistered Users</th><th>FTP Data</th><th>GDPR Compliance</th> |
| 142 | + </tr> |
| 143 | + </thead> |
| 144 | + <tbody> |
| 145 | + <tr> |
| 146 | + <td>User data on UseGalaxy.eu (i.e. datasets, histories) will be available as long |
| 147 | + as they are not deleted by the user. Once marked as deleted the datasets will |
| 148 | + be permanently removed within 14 days. If the user "purges" the dataset in the |
| 149 | + Galaxy, it will be removed immediately, permanently. |
| 150 | + |
| 151 | + An <a href="https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform" target="_blank">extended quota can be requested</a> |
| 152 | +for a limited time period in special cases. |
| 153 | + </td> |
| 154 | + <td>Processed data will only be accessible during one browser session, using a |
| 155 | + cookie to identify your data. This cookie is not used for any other purposes |
| 156 | + (e.g. tracking or analytics). |
| 157 | + |
| 158 | + If UseGalaxy.eu service is not accessed for 90 days, those datasets will be |
| 159 | + permanently deleted. |
| 160 | + </td> |
| 161 | + <td>Any user data uploaded to our <a href="https://galaxyproject.eu/ftp/">FTP server</a> should be imported into Galaxy as soon |
| 162 | + as possible. Data left in FTP folders for more than 3 months, will be deleted. |
| 163 | + </td> |
| 164 | + <td>The Galaxy service complies with the EU General Data Protection Regulation |
| 165 | + (GDPR). You can read more about this on our |
| 166 | + <a href="https://usegalaxy.eu/terms/">Terms and Conditions</a>.</td> |
| 167 | + </tr> |
| 168 | + </tbody> |
| 169 | + </table> |
| 170 | + |
| 171 | + |
| 172 | + |
| 173 | +<!-- <h4>Registered Users</h4> |
| 174 | +
|
| 175 | +User data on UseGalaxy.eu (i.e. datasets, histories) will be available as long |
| 176 | +as they are not deleted by the user. Once marked as deleted the datasets will |
| 177 | +be permanently removed within 14 days. If the user "purges" the dataset in the |
| 178 | +Galaxy, it will be removed immediately, permanently. |
| 179 | +
|
| 180 | +An <a href="https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform" target="_blank">extended quota can be requested</a> |
| 181 | +for a limited time period in special cases. |
| 182 | +
|
| 183 | +<h4>Unregistered Users</h4> |
| 184 | +
|
| 185 | +Processed data will only be accessible during one browser session, using a |
| 186 | +cookie to identify your data. This cookie is not used for any other purposes |
| 187 | +(e.g. tracking or analytics). |
| 188 | +
|
| 189 | +If UseGalaxy.eu service is not accessed for 90 days, those datasets will be |
| 190 | +permanently deleted. |
| 191 | +
|
| 192 | +<h4>FTP Data</h4> |
| 193 | +
|
| 194 | +Any user data uploaded to our <a href="https://galaxyproject.eu/ftp/">FTP server</a> should be imported into Galaxy as soon |
| 195 | +as possible. Data left in FTP folders for more than 3 months, will be deleted. |
| 196 | +
|
| 197 | +<h4>GDPR Compliance</h4> |
| 198 | +
|
| 199 | +The Galaxy service complies with the EU General Data Protection Regulation |
| 200 | +(GDPR). You can read more about this on our |
| 201 | +<a href="https://usegalaxy.eu/terms/">Terms and Conditions</a>. |
| 202 | + --> |
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| 245 | + <p>UseGalaxy.eu is maintained largely by the <a href="/freiburg/">Freiburg Galaxy Team</a> but also collectively by groups and individuals from across Europe. All of the member sites in this repository contribute to the European Galaxy Project. |
| 246 | +For <strong>acknowledgement</strong>, please refer to the <a href="/about">About</a> section. |
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