1_beginner.yml

id: beginner
title: Learn to use Galaxy for single-cell RNA-seq analysis
tabs:
  - id: pathway
    title: Learning pathways
    heading_html: >
      Connected tutorials to train you to perform single-cell analysis fast!
    content:
      - title_html: For first time Galaxy users
        description_html: >
          <p>
            Follow this learning pathway to learn how to use Galaxy and how to do single-cell RNA-seq analysis.
          </p>
        button_link: "https://training.galaxyproject.org/training-material/learning-pathways/intro_single_cell.html"
      - title_html: For experienced Galaxy users
        description_html: >
          <p>
            Follow this learning pathway to learn how to make analytical decisions in performing single-cell RNA-seq analysis and interpreting the data.
          </p>
        button_link1: "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-intro/slides.html"
        button_html1: "Introductory slides"
        button_link2: "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-trajectories/slides.html"
        button_html2: "Trajectories slides"
        button_link: "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html"
        button_link: "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html"
      - title_html: From tutorial data to real, messy, analytical decision-making
        description_html: >
          <p>
            Analysing real data
          </p>
        button_link: "https://training.galaxyproject.org/training-material/learning-pathways/beyond_single_cell.html"
  - id: training
    title: Importing public data
    heading_html: >
      Using public data is free! Learn how to retrieve data from common sources.
    content:
      - title_html: Importing files from public atlases
        description_html: >
          <p>
            Learn how to import data from common public atlases.
          </p>
        button_link: "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/EBI-retrieval/tutorial.html"
      - title_html: Importing from NCBI/GEO
        description_html: >
          <p>
            Guides you in importing data from the NCBI/GEO repository, including how to get metadata into your object.
          </p>
        button_link: "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html"
  - id: train
    title: Converting data
    heading_html: >
      Single-cell data comes in many formats. Here we demystify them and help you interconvert between formats.
    content:
      - title_html: Converting between formats
        description_html: >
          <p>
            From Seurat to Scanpy, from Matrix to Monocle, find common conversions here!
          </p>
        button_link: "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html"
  - id: help
    title: Help
    content:
      - title_html: How can I talk to other single cell analysts in the Galaxy community?
        description_html: >
          <p>
            Embed this snippet here: https://training.galaxyproject.org/training-material/topics/single-cell/faqs/#tip-how-can-i-talk-with-other-users
          </p>
        button_html: More info
        button_link: https://training.galaxyproject.org/training-material/topics/single-cell/faqs/#tip-how-can-i-talk-with-other-users
      - title_html: How can I troubleshoot?
        description_html: >
          <p>
            Embed this snippet here: https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html#troubleshooting-errors
          </p>
        button_html: More info
        button_link: https://training.galaxyproject.org/training-material/topics/single-cell/faqs/#tip-how-can-i-talk-with-other-users
      - title_html: Is there a help forum?
        description_html: >
          <p>
            <i class="fa fa-question-circle-o" aria-hidden="true"></i> [Single cell help forum](https://help.galaxyproject.org/tag/scrna)\
          </p>
        button_html: Help forum
        button_link: https://help.galaxyproject.org/tag/scrna
      - title_html: Can I upload sensitive data?
        description_html: >
          <p>
            No, do not upload personal or sensitive, such as human health or clinical data. Please see our <a href="/about#data-privacy">Data Privacy</a> page for definitions of sensitive and health-related information.
          </p>
          <p>
            Please also make sure you have read our <a href="/about#terms-of-service">Terms of Service</a>, which covers hosting and analysis of research data.
          </p>
      - title_html: Is my data private?
        description_html: >
          <p>
            Please read our <a href="/about#data-privacy">Privacy Policy</a> for information on your personal data and any data that you upload.
          </p>
      - title_html: How can I increase my storage quota?
        description_html: >
          <p>
            Please submit a quota request if your Galaxy  account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request.
          </p>
        button_html: Request
        button_link: /request/quota
      - title_html: Galaxy {{ site_name }} support
        description_html: >
          <p>
            Any user of Galaxy {{ site_name }} can request support through an online form.
          </p>
        button_html: Request support
        button_link: /request/support