Using Galaxy and Managing your Data

A collection of microtutorials explaining various features of the Galaxy user interface and manipulating data within Galaxy.

Material

Uploading Data

These tutorials will help you get data into Galaxy, before you analyse it.

Lesson Slides Hands-on Galaxy instances
Getting data into Galaxy
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Rule Based Uploader
tutorial
Rule Based Uploader: Advanced
tutorial
SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis
plain text tutorial

Galaxy Features

Learn how to use Galaxy efficiently

Lesson Slides Hands-on Galaxy instances
Extracting Workflows from Histories
tutorial
Searching Your History
tutorial
Understanding Galaxy history system
tutorial

Making Data Manageable

Now that you have data in Galaxy, let's make it easier to work with through collections and structured data.

Lesson Slides Hands-on Galaxy instances
Group tags for complex experimental designs
tutorial
Multisample Analysis
tutorial
Name tags for following complex histories
tutorial
Using dataset collections
tutorial

Analysing Data

Some advanced topics in data analyis.

Lesson Slides Hands-on Galaxy instances
Automating Galaxy workflows using the command line
tutorial
Creating, Editing and Importing Galaxy Workflows
tutorial
InterMine integration with Galaxy
tutorial
JupyterLab in Galaxy
tutorial
RStudio in Galaxy
tutorial
Use Jupyter notebooks in Galaxy
tutorial
Using Workflow Parameters
tutorial

Download and free up space

Once you are done with your analyses in Galaxy, it's time to download your data and free up space.

Lesson Slides Hands-on Galaxy instances
Downloading and Deleting Data in Galaxy
tutorial

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

Maintainers

This material is maintained by:

AvatarJennifer Hillman-JacksonAvatarHelena Rasche

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Simon BrayWolfgang MaierMarius van den BeekSimon GladmanHelena RascheDave ClementsAnne PajonMaria DoyleSaskia HiltemannDaniela ButanoYo YehudiAnne FouillouxAnton NekrutenkoBérénice BatutFotis E. PsomopoulosToby HodgesJohn ChiltonJon TrowAdelaide RhodesMiguel RoncoroniMartin ČechDelphine Lariviere