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single cell Galaxy{:width="25%"} Human Cell Atlas{:width="50%"}

Welcome to the Single Cell Omics Lab!

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The Single Cell Omics and The Human Cell Atlas{:target="_blank"} 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.

This service is a joint project between different groups from the Earlham Institute{:target="_blank"}, the Gene Expression Team at EMBL-EBI, the Teichmann Team at the Wellcome Sanger Institute, EMBL the Sorbonne University, Peter MacCallum Cancer Centre and the University of Freiburg.

The server is part if the European Galaxy server and is maintained by the RNA Bioinformatics Center (RBC){:target="_blank"} as part of de.NBI{:target="_blank"} and ELIXIR{:target="_blank"}.

Content

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  1. TOC {:toc}

Get started with #single-cell

Are you new to Galaxy, or returning after a long time, and looking for help to get started?

You may be interested in the following resources:

[Guided tour]({{ page.website }}/tours/core.galaxy_ui) through Galaxy's user interface.
Learning pathway for getting to grips with Galaxy and single cell
Single cell help forum
Single cell Galaxy user community chat room

Training

Want to learn even more about #single-cell analyses? You can check out our single cell training page within the wider Galaxy Training Network.

Single cell training material
the Galaxy Training Network

<iframe src="https://training.galaxyproject.org/training-material/tags/single-cell/embed.html" height="600px" width="100%" class="gtn-embed" frameborder="0"></iframe>

Workflows

In addition to our fantastic training materials, we encourage users to share their workflows!

Tag your workflows with #single-cell and share publicly with other users! {: .alert.alert-success}

You can see shared workflows below.

<iframe src="https://training.galaxyproject.org/training-material/workflows/embed.html?query=single-cell" height="600px" width="100%" class="gtn-embed" frameborder="0"></iframe>

Asking for help

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!

  1. General help forum or for single-cell specific questions, Single cell help forum
  2. Single cell Galaxy user community chat room
  3. Galaxy Training Community chat
  4. Usegalaxy.eu chat
  5. Usegalaxy.org chat

Asking for tools

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:

Tool Requests from Users

Join the Single Cell Community of Practice

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!

Go to our Community of Practice site to read more and join us!

Contributors