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
Getting data into Galaxy
slides
Rule Based Uploader
level level level
tutorial
Rule Based Uploader: Advanced
level level level
tutorial
SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis
slides tutorial

Galaxy Features

Learn how to use Galaxy efficiently

Lesson Slides Hands-on
Extracting Workflows from Histories
tutorial
Searching Your History
level level level
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
Group tags for complex experimental designs
tutorial
Multisample Analysis
level level level
tutorial
Name tags for following complex histories
tutorial
Using dataset collections
level level level
tutorial

Analysing Data

Some advanced topics in data analyis.

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

Jennifer Hillman-JacksonJennifer Hillman-Jackson Helena RascheHelena 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 BraySimon Bray Wolfgang MaierWolfgang Maier Marius van den BeekMarius van den Beek Simon GladmanSimon Gladman Helena RascheHelena Rasche Dave ClementsDave Clements Anne PajonAnne Pajon Maria DoyleMaria Doyle Saskia HiltemannSaskia Hiltemann Daniela ButanoDaniela Butano Yo YehudiYo Yehudi Anne FouillouxAnne Fouilloux Anton NekrutenkoAnton Nekrutenko Bérénice BatutBérénice Batut Fotis E. PsomopoulosFotis E. Psomopoulos Toby HodgesToby Hodges John ChiltonJohn Chilton Jon TrowJon Trow Adelaide RhodesAdelaide Rhodes Martin ČechMartin Čech Delphine LariviereDelphine Lariviere