Using Galaxy and Managing your Data — Editorial Board Home

This is a new, experimental "Editorial Board Home" for a given topic. It is intended to provide a single place for maintainers and editorial board members to find out key information about their topic and identify action items.

Editorial Board

orcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoHelena Rasche avatar Helena Rasche

Action Items

Item Status Why you should do this
Summary Done ✅ Provide a sufficiently detailed summary of the topic to let learners know what they're learning about in this topic.
Sufficient Editorial Board Members More required ❌ Having multiple people sharing the burden of being responsible for a specific topic can reduce board member burn-out in the long term.
Enable Subtopics Done ✅ Subtopics help organize the content and make it easier to navigate.
Annotate Funders Done ✅ (1 funders) By annotating the funders of your topic's materials, you make it easier to write your grant reports later
Learning Pathway CTA Pending ❌ By providing a Learning Pathway CTA, we can help guide learners to the best resources for learning about this topic.

Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
Getting data into Galaxy ❌ ❌ ❌ ❌ ❌
Rule Based Uploader ❌ ✅ ✅ ✅ ❌
Rule Based Uploader: Advanced ❌ ✅ ❌ ❌ ❌
SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis ❌ ✅ ❌ ✅ ❌
Searching Your History ❌ ❌ ❌ ❌ ❌
Understanding Galaxy history system ✅ ❌ ❌ ❌ ❌
Group tags for complex experimental designs ❌ ❌ ❌ ❌ ❌
Name tags for following complex histories ❌ ❌ ❌ ❌ ❌
Using dataset collections ❌ ❌ ❌ ✅ ❌
Automating Galaxy workflows using the command line ❌ ✅ ❌ ❌ ❌
Creating high resolution images of Galaxy Workflows ✅ ✅ ❌ ✅ ❌
Creating, Editing and Importing Galaxy Workflows ❌ ❌ ❌ ❌ ❌
Extracting Workflows from Histories ❌ ❌ ❌ ❌ ❌
Galaxy workflows in Dockstore ❌ ❌ ❌ ✅ ❌
Using Workflow Parameters ❌ ❌ ❌ ❌ ❌
Workflow Reports ✅ ❌ ❌ ❌ ❌
InterMine integration with Galaxy ✅ ❌ ❌ ✅ ❌
JupyterLab in Galaxy ✅ ❌ ❌ ❌ ❌
RStudio in Galaxy ✅ ❌ ✅ ❌ ❌
Use Jupyter notebooks in Galaxy ❌ ❌ ❌ ✅ ❌
Downloading and Deleting Data in Galaxy ❌ ❌ ❌ ❌ ❌
Submitting sequence data to ENA ❌ ✅ ❌ ✅ ❌

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
Automating Galaxy workflows using the command line vcf2lineage Dec 23, 2024 1 ❌ ❌ ❌
Creating, Editing and Importing Galaxy Workflows Tutorial workflow Dec 23, 2024 1 ❌ ❌ ❌
Creating, Editing and Importing Galaxy Workflows Subworkflow Dec 23, 2024 1 ❌ ❌ ❌
Using Workflow Parameters Select First N Lines Dec 23, 2024 1 ❌ ❌ ❌
Workflow Reports GTN Training: Workflow Reports - Galaxy 101 For Everyone Dec 23, 2024 2 ❌ ❌ ❌
Workflow Reports GTN Training: Workflow Reports Dec 23, 2024 1 ❌ ✅ ❌
InterMine integration with Galaxy Intermine import/export Dec 23, 2024 1 ❌ ❌ ❌
Submitting sequence data to ENA GTN_ENA_upload_workflow Dec 23, 2024 1 ❌ ❌ ❌

Your topic's Workflow Testing Results

Coming Soon™

Learning Pathways using materials from this Topic

GTN Logo on a spiral galaxy background with text galaxy admin training
Admin Training Course

Learn how to setup, configure, and maintain your own Galaxy server. This learning pathway will guide you through all the steps required to setup your own Galaxy server with Ansible, configuring it, and making it production ready.

Galaxy administrators 5-day course admin
Image of cells in different coloured clusters
Applying single-cell RNA-seq analysis

Gone is the pre-annotated, high quality tutorial data - now you have real, messy data to deal with. You have decisions to make and parameters to decide. This learning pathway challenges you to replicate a published analysis as if this were your own dataset. You will be introduced to a few more tools available for scRNA-seq in Galaxy. Finally, if...

intermediate single-cell
Image of cells in different coloured clusters
Introduction to Galaxy and Single Cell RNA Sequence analysis

This learning path aims to teach you the basics of Galaxy and analysis of Single Cell RNA-seq data. You will learn how to use Galaxy for analysis, and an important Galaxy feature for iterative single cell analysis. You’ll tbe guided through the general theory of single analysis and then perform a basic analysis of 10X chromium data. For support throughout...

beginner single-cell
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Applying single-cell RNA-seq analysis in Coding Environments

Gone is the pre-annotated, high quality tutorial data - now you have real, messy data to deal with. You have decisions to make and parameters to decide. This learning pathway challenges you to replicate a published analysis as if this were your own dataset. You will perform this analysis in coding environments hosted on Galaxy, instead of Galaxy’s button-based tool...

advanced single-cell
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Events using materials from this Topic

TODO once this is merged: https://github.com/galaxyproject/training-material/pull/4963

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