Register training material
23 materials found

Keywords: R-programming  or galaxy-interface 


Hands-on for 'JupyterLab in Galaxy' tutorial

The questions this addresses are:
- How can I manipulate data using JupyterLab in Galaxy?
- How can I start a notebook in JupyterLab?
- How can I import/export dataset from/to my history to/from the notebook?
- How can I save my notebook to my history?

The objectives are:
- Launch...

Keywords: galaxy-interface, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Rule Based Uploader: Advanced' tutorial

The questions this addresses are:
- How to use the rule based uploader to create complex collections

The objectives are:
- Learn even more about the Rule Based Uploader

Keywords: galaxy-interface, collections, tags

Resource type: hands-on tutorial

Hands-on for 'Workflow Reports' tutorial

The questions this addresses are:
- What are workflow reports?
- How can I view a workflow report?
- How can I customize a workflow report?
- How can I share a workflow report with others?

The objectives are:
- Understanding, viewing and creating workflow reports

Keywords: galaxy-interface, workflows

Resource type: hands-on tutorial

Hands-on for 'Extracting Workflows from Histories' tutorial

The questions this addresses are:
- What is a workflow?
- How can I create a workflow based on my analysis history?

The objectives are:
- Learn how to extract a workflow from a Galaxy history
- Learn how to change a workflow using the workflow editor

Keywords: galaxy-interface, workflows

Resource type: hands-on tutorial

Hands-on for 'Automating Galaxy workflows using the command line' tutorial

The questions this addresses are:
- How can I schedule and run tens or hundreds of Galaxy workflows easily?
- How can I automate my analyses when large amounts of data are being produced daily?

The objectives are:
- Learn to use the planemo run subcommand to run workflows from the command...

Keywords: galaxy-interface, workflows, variant-analysis, covid19

Resource type: hands-on tutorial

Hands-on for 'SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis' tutorial

The questions this addresses are:
- How can I search SRA SARS-CoV-2 metadata from within Galaxy?
- How can I import SRA aligned read files and extract the data in my format of choice?
- How can I import vcf files into Galaxy that have been generated for these Runs?

The objectives are:
-...

Keywords: galaxy-interface, ncbi, covid19

Resource type: hands-on tutorial

Hands-on for 'Downloading and Deleting Data in Galaxy' tutorial

The questions this addresses are:
- How can I efficiently download my data from Galaxy once I've completed my analyses?
- How do I delete old data to make more room in my quota?

The objectives are:
- Have a greater knowledge of how Galaxy handles data downloads and deletions
- Be able to...

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'Submitting sequence data to ENA' tutorial

The questions this addresses are:
- How do you submit raw sequence reads and assembled genomes to the European Nucleotide Archive?

The objectives are:
- Submit raw sequencing reads and metadata to ENA's test server
- Submit consensus sequence and metadata to ENA's test server

Keywords: galaxy-interface, covid19

Resource type: hands-on tutorial

Hands-on for 'RStudio in Galaxy' tutorial

The questions this addresses are:
- How can I manipulate data using R in Galaxy?

The objectives are:
- Launch RStudio in Galaxy

Keywords: galaxy-interface, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Group tags for complex experimental designs' tutorial

The questions this addresses are:
- What are group tags?
- How can I use group tags to perform multi-factor analyses with collections

The objectives are:
- Learn how to set group tags
- Learn how to select group tags in tools

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'Creating, Editing and Importing Galaxy Workflows' tutorial

The questions this addresses are:
- How can you construct Galaxy workflows from scratch?
- How can you label outputs?
- How can you include workflows in workflows?
- How can you tag workflows?
- How can you manage tool versions?
- How can you manage workflow versions?

The objectives...

Keywords: galaxy-interface, workflows

Resource type: hands-on tutorial

Hands-on for 'Use Jupyter notebooks in Galaxy' tutorial

The questions this addresses are:
- How to use a Jupyter Notebook in Galaxy

The objectives are:
- Learn about the Jupyter Interactive Environment

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'InterMine integration with Galaxy' tutorial

The questions this addresses are:
- How to export your query results from your InterMine of choice to Galaxy?
- How to export a list of identifiers from Galaxy to your InterMine of choice?

The objectives are:
- Learn how to import/export data from/to InterMine instances
- Understand the...

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'Rule Based Uploader' tutorial

The questions this addresses are:
- How to use the rule based uploader to create complex collections

The objectives are:
- Learn about the Rule Based Uploader

Keywords: galaxy-interface, collections, tags

Resource type: hands-on tutorial

Hands-on for 'Using dataset collections' tutorial

The questions this addresses are:
- How to manipulate large numbers of datasets at once?

The objectives are:
- Understand and master dataset collections

Keywords: galaxy-interface, collections

Resource type: hands-on tutorial

Hands-on for 'Using Workflow Parameters' tutorial

The questions this addresses are:
- What are Workflow Parameters
- How can I define and use Workflow Parameters
- How can I read Parameters from Datasets

The objectives are:
- Learn how to use Workflow Parameters to improve your Workflows

Keywords: galaxy-interface, workflows

Resource type: hands-on tutorial

Hands-on for 'Name tags for following complex histories' tutorial

The questions this addresses are:
- What are name tags or hash tags?
- How can I use them to keep track of my data?

The objectives are:
- Learn how to set name tags
- Learn how they are propagated

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'Understanding Galaxy history system' tutorial

The questions this addresses are:
- How do Galaxy histories work?

The objectives are:
- Gain understanding on navigating and manipulating histories

Keywords: galaxy-interface

Resource type: hands-on tutorial

Hands-on for 'Searching Your History' tutorial

The questions this addresses are:
- How can you find your datasets?
- How to search by file type?
- What filters are available to you?

The objectives are:
- Feel confident in searching your history

Keywords: galaxy-interface

Resource type: hands-on tutorial

Slides for 'Introduction to SRA Aligned Read Format and Cloud Metadata for SARS-CoV-2' tutorial

The questions this addresses are:
- What is the SRA Aligned Read Format
- How can I use it?

The objectives are:
- Understand which data and metadata types are available for SARS-CoV-2 SRA runs in the cloud.
- Understand what SRA Aligned Read Format is and what can you do with it.
-...

Keywords: galaxy-interface, ncbi, covid19

Resource type: slides

Slides for 'Submitting SARS-CoV-2 sequences to ENA' tutorial

The objectives are:
- Introduce the European Nucleotide Archive (ENA)
- Learn the requirements to submit raw SARS-CoV-2 sequences to ENA in Galaxy
- Overview ENA's metadata model and how metadata objects are linked

Keywords: galaxy-interface

Resource type: slides

Slides for 'Getting data into Galaxy' tutorial

The questions this addresses are:
- How do I get my data into Galaxy?
- How do I get public data into Galaxy?

Keywords: galaxy-interface

Resource type: slides

Slides for 'Galaxy workflows in Dockstore' tutorial

The objectives are:
- What is Dockstore?
- Why use Dockstore?
- How to find workflows on Dockstore?
- How to launch workflows from Dockstore?
- Getting started with Galaxy workflows on Dockstore
- Register your Galaxy workflow on Dockstore

Keywords: galaxy-interface

Resource type: slides