Welcome to the Galaxy Training Video Library!

This page shows you the full library of available GTN video tutorials, you can use these for self-study, courses, and more! Below are all of the individual videos, but some videos are part of multi-video “sessions” which can be found in the session library

Multi-Video Sessions Training Modules Adding Videos


All Training Videos

Here is the full list of all individual training videos

Admin

Tutorial Video

Length: 2 hours 50 minutes
Captions: Nate Coraor, Helena Rasche
Created: 1 March 2022
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Have an understanding of how Galaxy's Ansible roles are structured and interact with one another
  • Be able to use an Ansible playbook to install different flavors of Galaxy for different purposes
Go to the video page to see all versions.

Speakers

Lecture Video

Length: 5 minutes
Captions: Martin Čech
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Learn Ansible basics
  • Write a simple role
  • Install a role from Ansible Galaxy
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 61 minutes
Captions: Martin Čech
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Learn Ansible basics
  • Write a simple role
  • Install a role from Ansible Galaxy
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 31 minutes
Captions: Catherine Bromhead, Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 3 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Have an understanding of what CVMFS is and how it works
  • Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
  • Configure your Galaxy to use these reference genomes and indices
  • Use an Ansible playbook for all of the above.
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 23 minutes
Captions: Simon Gladman
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Have an understanding of what CVMFS is and how it works
  • Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
  • Configure your Galaxy to use these reference genomes and indices
  • Use an Ansible playbook for all of the above.
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 22 minutes
Captions: Helena Rasche, Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Setup a data library
  • Manage permissions
  • Import data from disk
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 2 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Learn gxadmin basics
  • See some queries and learn how they help debug production issues
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 44 minutes
Captions: Anthony Bretaudeau, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Supported Servers:
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Speaker

Tutorial Video

Length: 31 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Know how to map tools to job destinations
  • Be able to use the dynamic job runner to make arbitrary destination mappings
  • Understand the job resource selector config and dynamic rule creation
  • The various ways in which tools can be mapped to destinations, both statically and dynamically
  • How to write a dynamic tool destination (DTD)
  • How to write a dynamic python function destination
  • How to use the job resource parameter selection feature
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Speaker

Tutorial Video

Length: 6 minutes
Captions: Beatriz Serrano-Solano
Created: 15 February 2021
Materials:
Support:
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Speaker

Lecture Video

Length: 2 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Go to the video page to see all versions.

Speaker

Lecture Video

Length: 2 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Setup InfluxDB
  • Setup Telegraf
  • Setup Grafana
  • Create several charts
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 73 minutes
Captions: Saskia Hiltemann, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Setup InfluxDB
  • Setup Telegraf
  • Setup Grafana
  • Create several charts
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 18 minutes
Captions: Catherine Bromhead
Created: 15 February 2021
Materials:
Support:
Go to the video page to see all versions.

Speaker

Lecture Video

Length: 14 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Have an understanding of what Pulsar is and how it works
  • Install and configure a RabbitMQ message queueing server
  • Install and configure a Pulsar server on a remote linux machine
  • Be able to get Galaxy to send jobs to a remote Pulsar server
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 1 hour 28 minutes
Captions: Helena Rasche
Created: 28 June 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Have an understanding of what Pulsar is and how it works
  • Install and configure a RabbitMQ message queueing server
  • Install and configure a Pulsar server on a remote linux machine
  • Be able to get Galaxy to send jobs to a remote Pulsar server
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

Running jobs in Apptainer
Length: 43 minutes
Captions: Cristóbal Gallardo, Simon Gladman
Created: 28 June 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Configure your Galaxy to use Apptainer and BioContainers for running jobs
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 24 minutes
Captions: Helena Rasche, Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Setup TIaaS
  • Request and manage trainings
  • Join a training
Go to the video page to see all versions.

Speaker

Lecture Video

Length: 17 minutes
Captions: Catherine Bromhead
Created: 28 June 2021
Materials:
Support:
Learning Objectives:
  • Learn about Ephemeris
  • Extract a list of tools from a workflow
  • Install these tools on a given Galaxy
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 27 minutes
Captions: Catherine Bromhead
Created: 28 June 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Learn about Ephemeris
  • Extract a list of tools from a workflow
  • Install these tools on a given Galaxy
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

Here you’ll learn to setup TUS an open source resumable file upload server to process uploads for Galaxy. We use an external process here to offload the main Galaxy processes for more important work and not impact the entire system during periods of heavy uploading.
Length: 7 minutes
Captions: Helena Rasche
Created: 11 March 2022
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Setup TUSd
  • Configure Galaxy to use it to process uploads
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 36 minutes
Captions: Simon Gladman, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Understand how to find the current Galaxy server version you are using
  • How to find the latest release version
  • How to backup the Galaxy server database and why it's a good idea
  • How to upgrade the Galaxy server to a new version
Go to the video page to see all versions.

Speaker

Lecture Video

Length: 4 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Learn the Galaxy user/group management and assign Quotas.
  • Understand the Role Based Access Control (RBAC) of Galaxy.
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Speaker

Tutorial Video

Length: 4 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
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Speaker

Lecture Video

Description:

This supplementary welcome will give you additional details that are needed for the week.

Please note that when you use the mentioned /completed command, you do not need to specify a history URL. Just /completed is sufficient.
Length: 4 minutes
Captions: Helena Rasche
Created: 15 February 2021
Support:
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Speakers

Assembly

Tutorial Video

Description:

This tutorial guides you through the preprocessing of sequencing data of bronchoalveolar lavage fluid (BALF) samples obtained from early COVID-19 patients in China. Since such samples are expected to be contaminated signficantly with human sequenced reads, the goal is to enrich the data for SARS-CoV-2 reads by identifying and discarding reads of human origin before trying to assemble the viral genome sequence.
Length: 25 minutes
Captions: Mehmet Tekman
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

In this tutorial, we will walk you through an assembly of a large genome, such as a plant or animal genome.
Length: 25 minutes
Captions: Anna Syme
Created: 16 May 2023
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Assemble a large genome from long reads
  • Polish the assembly
  • Assess the quality of the assembly
Go to the video page to see all versions.

Speaker

Lecture & Tutorial Video

Description:

In this tutorial, you will assemble a chloroplast genome using a combination of short and long read data.
Length: 35 minutes
Captions: Anna Syme
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Assemble a chloroplast genome from long reads
  • Polish the assembly with short reads
  • Annotate the assembly and view
  • Map reads to the assembly and view
Go to the video page to see all versions.

Speaker

Lecture Video

Description:

This lecture walks you through the basic concepts involved in assembling a genome from short-read sequencing data.
Length: 25 minutes
Captions: Saskia Hiltemann, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • assemble some paired end reads using Velvet
  • examine the output of the assembly.
Go to the video page to see all versions.

Speaker

Demo Video

Description:

This demo walks you through running the VGP Genome Assembly workflows, rather than the whole tutorial (as most GTN videos do)
Length: 10 minutes
Captions: Delphine Lariviere
Created: 13 March 2022
Materials:
Support:
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Speaker

Video

Description:

In this tutorial, we will learn how to run metagenomic assembly tool and evaluate the quality of the generated assemblies. To do that, we will use data from the study: Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem. For an in-depth analysis of the structure and functions of the coffee microbiome, a temporal shotgun metagenomic study (six time points) was performed. The six samples have been sequenced with Illumina MiSeq utilizing whole genome sequencing.
Length: 1 hour
Captions: Bérénice Batut, Sophia Hampe
Created: 2 May 2023
Materials:
Support:
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Speaker

Climate

Lecture Video

Description:

This lecture provides a brief overview of FATES
Length: 7 minutes
Captions: Anne Fouilloux
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Setting up a CLM-FATES case.
  • Customizing your run.
  • Interactive visualization with Panoply.
  • Automating your analyzes and visualisations of your CLM-FATES case.
  • Creating multi-case scenarios.
  • Composing, executing and publishing CML-FATES workflow.
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

This tutorial will walk you through a Galaxy analysis step by step
Length: 1 hour 20 minutes
Captions: Sébastien Fouilloux
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Setting up a CLM-FATES case.
  • Customizing your run.
  • Interactive visualization with Panoply.
  • Automating your analyzes and visualisations of your CLM-FATES case.
  • Creating multi-case scenarios.
  • Composing, executing and publishing CML-FATES workflow.
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

In this tutorial, we will learn about Xarray, one of the most used Python library from the Pangeo ecosystem.

We will be using data from Copernicus Atmosphere Monitoring Service and more precisely PM2.5 (Particle Matter < 2.5 μm) 4 days forecast from December, 22 2021. Parallel data analysis with Pangeo is not covered in this tutorial.
Length: 17 minutes
Captions: Anne Fouilloux
Created: 3 March 2022
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Learn to get metadata information using Xarray Galaxy Tools
  • Learn to select data
  • Learn to visualize data
  • Learn to filter, make reduction operations (mean, max, min)
  • Learn to resample my data
  • Learn to cite and contribute to Pangeo
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

In this tutorial, you will learn how to manipulate netCDF data files using Xarray Galaxy Tools. NetCDF stands for network Common Data Form and is one of the most popular file format in climate science. It is used for storing multidimensional scientific data variables such as temperature or humidity, and metadata can be added to facilitate sharing of netCDF data. netCDF is widely used outside the Climate Science community and each community has its own set of conventions, especially for metadata. The Climate and Forecast metadata convention, also called CF-convention is used by the Climate community and is designed to promote the processing and sharing of netCDF files.
Length: 1 hour 20 minutes
Captions: Anne Fouilloux
Created: 3 March 2022
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Understand what Pangeo and Xarray are
  • Learn to get metadata information using Xarray Galaxy Tools
  • Learn to select data
  • Learn to visualize geographical data on a map
  • Learn to filter, make reduction operations (mean, max, min)
  • Learn to resample my data
Go to the video page to see all versions.

Speaker

Community

Welcome Video

Description:

This short video gives an overview of the worldwide Galaxy community, and different ways you can get involved! Video created by Beatriz Serrano-Solano.
Length: 5 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
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Speaker

Computational chemistry

Tutorial Video

Description:

Molecular dynamics (MD) is a method to simulate molecular motion by iterative application of Newton’s laws of motion. This tutorial provides an introduction to using high-throughput molecular dynamics to study protein-ligand interaction, as applied to the N-terminal domain of Hsp90 (heat shock protein 90).
Length: 1 hour 40 minutes
Captions: Simon Bray
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Learn about force-fields and MD parameterization
  • Learn how to conduct MD simulation and analysis for a protein-ligand system
  • Understand how different molecular interactions contribute to the binding affinity of various ligands for the Hsp90 protein.
Go to the video page to see all versions.

Speakers

Contributing

Lecture Video

Description:

This lecture goes through the process of how to create a slide deck, common things you should bear in mind while you’re writing them, and how to enable the amazing slides-to-video features for your slide decks! This video itself was produced automatically from the GTN’s slide decks, anyone making edits to these slides will cause them to be rebuilt, making organising videos for events easier than ever.
Length: 5 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Create a new set of slides
  • Add presenter comments
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

This tutorial will go through all of the steps of creating a simple tutorial and contributing it to the GTN.
Length: 42 minutes
Captions: Engy Nasr
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Create a tutorial from scratch
  • Link a tutorial to a topic
  • Create hands-on
  • Add technical support for a tutorial
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

This tutorial will show you how you can preview your contributions to the GTN online using GitPod.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Preview the GTN website online via GitPod
  • Make changes to the GTN website and preview those changes
Go to the video page to see all versions.

Speaker

Event

Tutorial Video

Length: 9 minutes
Captions: Helena Rasche
Created: 15 February 2021
Support:
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Speaker

Lecture Video

Description:

Start here; we will go over all the important things to know to get the most out of this workshop
Length: 15 minutes
Captions: Saskia Hiltemann, Helena Rasche
Created: 15 February 2021
Materials:
Support:
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Speakers

Welcome Video

Description:

Start here! We will go over all the important things you need to know about this week!
Length: 15 minutes
Captions: Saskia Hiltemann
Created: 10 March 2022
Materials:
Support:
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Speakers

Welcome Video

Description:

Start here! We will go over all the important things you need to know about this week!
Length: 15 minutes
Captions: Saskia Hiltemann
Created: 16 May 2023
Materials:
Support:
Go to the video page to see all versions.

Speakers

Data science

Tutorial Video

Description:

An advanced tutorial covering downstream analysis of RNA-seq data using R.
Length: 1 hour
Captions: Keith Suderman, Nadia Goué
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Be able to load and explore the shape and contents of a tabular dataset using base R functions.
  • Understand factors and how they can be used to store and work with categorical data.
  • Apply common `dplyr` functions to manipulate data in R.
  • Employ the ‘pipe’ operator to link together a sequence of functions.
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

This tutorial will provide an introduction to using R with Rstudio in Galaxy.
Length: 50 minutes
Captions: Sébastien Fouilloux, Anne Fouilloux, Kaivan Kamali
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Know advantages of analyzing data using R within Galaxy.
  • Compose an R script file containing comments, commands, objects, and functions.
  • Be able to work with objects (i.e. applying mathematical and logical operators, subsetting, retrieving values, etc).
Go to the video page to see all versions.

Speaker

Galaxy interface

Demo Video

Description:

This tutorial will show you how you can start Rstudio from within Galaxy. This option is only available on Galaxy EU for the time being. If you are working on a different Galaxy server, you can use Rstudio Cloud (https://rstudio.cloud/)
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Go to the video page to see all versions.

Speaker

Demo Video

Length: 18 minutes
Captions: Saskia Hiltemann
Created: 19 May 2023
Materials:
Support:
Supported Servers: Possibly Working
Learning Objectives:
  • Gain understanding on navigating and manipulating histories
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Speaker

Tutorial Video

Length: 13 minutes
Captions: Delphine Lariviere
Created: 9 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Understand and master dataset collections
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Speaker

Lecture Video

Description:

This lecture will introduce the SRA Aligned Read format available in the cloud from SRA, as well as some accompanying metadata that can help you search and filter the data. This sessions is aimed specifically at SARS-CoV-2 runs in SRA.
Length: 15 minutes
Captions: Jonathan Trow
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content
  • Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

This tutorial will walk you through accessing and using SRA Aligned read format in Galaxy.
Length: 40 minutes
Captions: Jonathan Trow
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content
  • Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

Through a series of examples, this tutorial aims to familiarize the reader with building Galaxy collections from tabular data containing URLs, sample sheets, list of accessions or identifiers, etc..
Length: 22 minutes
Captions: Assunta DeSanto
Created: 15 February 2021
Materials:
Support:
Supported Servers: Possibly Working
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Speaker

Lecture & Tutorial Video

Description:

So you’ve used Galaxy workflows to analyze your SARS-CoV-2 samples? Learn in this tutorial how to export results to your favorite datastore.
Length: 10 minutes
Captions: Helena Rasche
Created: 9 August 2021
Support:
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Speaker

Tutorial Video

Description:

This is a more technical tutorial which will teach you how to run workflows from the command line and scale your analyses. If you are on Windows, you will need WSL/WSL2 setup before this session.
Length: 30 minutes
Captions: Simon Bray
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
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Speaker

Tutorial Video

Description:

To make a workflow reusable with slightly different settings you can define and use workflow parameters.
Length: 30 minutes
Captions: Marius van den Beek
Created: 6 July 2022
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Learn how to use Workflow Parameters to improve your Workflows
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Speaker

Tutorial Video

Description:

Learn how to view, customize and share Galaxy workflow reports
Length: 30 minutes
Captions: Saskia Hiltemann
Created: 6 July 2022
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Understanding, viewing and creating workflow reports
Go to the video page to see all versions.

Speaker

Dev

Lecture Video

Description:

TODO
Length: 15 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
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Speaker

Lecture Video

Description:

TODO
Length: 25 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
Go to the video page to see all versions.

Speaker

Lecture Series Video

Description:

TODO
Length: 17 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
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Speaker

Lecture Video

Description:

TODO
Length: 15 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
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Speaker

Lecture Video

Description:

TODO
Length: 45 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
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Speaker

Lecture Video

Description:

TODO
Length: 5 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
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Speaker

Lecture Video

Description:

TODO
Length: 25 minutes
Captions: Mallory Freeberg
Created: 15 February 2021
Materials:
Support:
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Speaker

Lecture Video

Description:

TODO
Length: 15 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
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Speaker

Lecture Video

Description:

TODO
Length: 35 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:

What to do when an API test fails.
Length: 23 minutes
Captions: John Davis
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:

This video covers working through the client linting error hit in the previous tutorial.
Length: 6 minutes
Captions: Beatriz Serrano-Solano
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:

What to do when your client throws a unit test failure.
Length: 6 minutes
Captions: Beatriz Serrano-Solano
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:

This is the first video in the Debugging Galaxy series.
Length: 11 minutes
Captions: Dave Clements
Created: 15 February 2021
Materials:
Support:
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Speakers

Tutorial Video

Description:

How to fix a runtime error
Length: 40 minutes
Captions: John Davis
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:

Selenium is used to test Galaxy development. Learn more about test failure and how to address them.
Length: 18 minutes
Captions: Assunta DeSanto, John Davis, Dave Clements, Beatriz Serrano-Solano
Created: 15 February 2021
Materials:
Support:
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Speaker

Lecture Video

Description:

A summary of wisdom to debug Galaxy with.
Length: 3 minutes
Captions: Dave Clements
Created: 15 February 2021
Materials:
Support:
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Speakers

Tutorial Video

Description:

What to do when a unit test fails.
Length: 14 minutes
Captions: John Davis
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:
  1. The first step to adding a tool to Galaxy, is to add it to (Bio)Conda. This tutorial will show you how to do that.
  2. Planemo is the Galaxy tool development kit, and will make your tool development process a lot easier! This tutorial will show you how to use Planemo to start the tool wrapping process, and covers the general structure of a Galaxy tool wrapper.
  3. You are now ready to start writing your tool wrapper! This video will show you how.
  4. Each tool wrapper also needs a .shed.yml file, which contains some metadata about the tool.
  5. Here you will learn how to test Galaxy tools using Planemo.
  6. Here you will learn how to publish tools in public tool repositories.
Length: 50 minutes
Captions: Cristóbal Gallardo, Alex Ostrovsky
Created: 18 May 2023
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Learn how to make and deploy a conda package
  • Understand how to write a Galaxy tool wrapper
  • Be able to use a tool wrapper locally
  • Be able to test the tool wrapper
  • Learn how to add tools to the Galaxy toolshed and make them available to any user
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Speakers

Video

Description:

Hands on demonstration for the Introductory tutorial. Create, run and update a “Hello World” tool in Galaxy
Length: 7 minutes
Captions: Ross Lazarus
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Further develop your ToolFactory Skills
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Speaker

Video

Description:

ToolFactory Presentation: Abstract tool interface code that wraps simple scripts can be generated using a Galaxy tool. If you haven’t already decided that the GTN tutorials linked below might be useful for your work, or if want to hear Ross’s opinions on tools, abstract interfaces and why they matter, this talk is for you.
Length: 30 minutes
Captions: Ross Lazarus
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Learn why you might want to use the ToolFactory development server
  • Watch a video demonstration and explore the generated code - Hello Galaxy Training Network!
  • Run it locally in Docker.
  • Install and explore the simple examples provided.
  • Modify and re-generate them to see how the changes affect the tool
  • Generate new simple Galaxy tools using your own scripts
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Speaker

Ecology

Lecture Video

Description:

Based on this OBITools official tutorial, you will learn here how to analyze DNA metabarcoding data produced on Illumina sequencers
Length: 1 hour 15 minutes
Captions: Yvan Le Bras
Created: 3 March 2022
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Deal with paired-end data to create consensus sequences
  • Clean, filter and anlayse data to obtain strong results
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Speaker

Lecture Video

Description:

This tutorial aims to present the PAMPA Galaxy workflow, how to use it to compute common biodiversity metrics from species abundance data and analyse it through generalized linear (mixed) models (GLM and GLMM). This workflow made up of 5 tools will allow you to process temporal series data that include at least year, location and species sampled along with abundance value and, finally, generate article-ready data products.
Length: 2 hours
Captions: Coline Royaux
Created: 3 March 2022
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Upload data from DATRAS portal of ICES
  • Pre-process population data with Galaxy
  • Learning how to use an ecological analysis workflow from raw data to graphical representations
  • Learning how to construct a Generalized Linear (Mixed) Model from a usual ecological question
  • Learning how to interpret a Generalized Linear (Mixed) Model
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Speaker

Lecture Video

Length: 1 hour
Captions: Olivier Norvez
Created: 3 March 2022
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Explore Biodiversity data with taxonomic, temporal and geographical informations
  • Have an idea about quality content of the data regarding statistical tests like normality or homoscedasticity and coverage like temporal or geographical coverage
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Speaker

Epigenetics

Lecture Video

Description:

This lecture will introduce the basic concepts involved in ATAC-Seq analysis.
Length: 15 minutes
Captions: Lucille Delisle
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Apply appropriate analysis and quality control steps for ATAC-Seq
  • Generate a heatmap of transcription start site accessibility
  • Visualise peaks for specific regions
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Speaker

Tutorial Video

Description:

This tutorial will walk you through a ATAC-Seq data analysis.
Length: 1 hour 50 minutes
Captions: Hans-Rudolf Hotz
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Apply appropriate analysis and quality control steps for ATAC-Seq
  • Generate a heatmap of transcription start site accessibility
  • Visualise peaks for specific regions
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Speaker

Galaxy intro

Demo Video

Description:

This demo videos shows you how you can run Interactive tools such as RStudio and Jupyter notebooks within Galaxy.
Length: 15 minutes
Captions: Saskia Hiltemann
Created: 7 July 2022
Support:
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Speaker

Lecture & Demo Video

Description:

This video will introduce the Galaxy data analysis platform, and give a short demo on how to use it.
Length: 10 minutes
Captions: Anton Nekrutenko
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:

In this tutorial, we will walk you through your first (toy) analysis in Galaxy. This tutorial is aimed at familiarizing you with the Galaxy platform, and some basic NGS concepts.
Length: 1 hour 30 minutes
Captions: Natalie Kucher
Created: 18 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
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Speaker

Galaxy

Demo Video

Description:

This demo videos shows you how you can run Interactive tools such as RStudio and Jupyter notebooks within Galaxy.
Length: 15 minutes
Captions: Saskia Hiltemann
Created: 7 July 2022
Support:
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Speaker

Lecture & Demo Video

Description:

This video will introduce the Galaxy data analysis platform, and give a short demo on how to use it.
Length: 10 minutes
Captions: Anton Nekrutenko
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:

In this tutorial, we will walk you through your first (toy) analysis in Galaxy. This tutorial is aimed at familiarizing you with the Galaxy platform, and some basic NGS concepts.
Length: 1 hour 30 minutes
Captions: Natalie Kucher
Created: 18 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
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Speaker

Tutorial Video

Description:

This video tutorial will provide a non-genomics based first look at the Galaxy platform, how to use it, and discusses how you can get support for your data analysis.
Length: 20 minutes
Captions: Alex Ostrovsky
Created: 1 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Familiarize yourself with the basics of Galaxy
  • Learn how to obtain data from external sources
  • Learn how to tag datasets
  • Learn how to run tools
  • Learn how histories work
  • Learn how to create a workflow
  • Learn how to share your work
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Speaker

Sars cov2

Lecture & Tutorial Video

Description:

So you’ve used Galaxy workflows to analyze your SARS-CoV-2 samples? Learn in this tutorial how to export results to your favorite datastore.
Length: 10 minutes
Captions: Helena Rasche
Created: 9 August 2021
Support:
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Speaker

Demo Video

Description:

In this demo you will get to know the ObservableHQ platform for interactive data visualization. You will see how covid19.galaxyproject.org uses it to build a dashboard for their SARS-CoV-2 analysis efforts and will learn how to customize this solution to fit your own purposes.
Length: 15 minutes
Captions: Assunta DeSanto
Created: 8 December 2021
Support:
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Speaker

Demo Video

Length: 10 minutes
Captions: Pia H., Assunta DeSanto
Created: 8 December 2021
Support:
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Speaker

Demo Video

Description:

See in this demo how, on usegalaxy.*, we’ve used Planemo and Bioblend to build and operate an automated SARS-CoV-2 genome surveillance system based on the Galaxy workflows for variant calling, consensus building and reporting.
Length: 40 minutes
Captions: Helena Rasche
Created: 9 August 2021
Support:
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Speaker

Tutorial Video

Description:

Get an overview of the workshop: production-ready Galaxy workflows for SARS-CoV-2 sequencing data, tools you should know to automate workflow execution, and how you combine all of it to turn Galaxy into a platform for genome-surveillance
Length: 13 minutes
Captions: Pia H.
Created: 9 August 2021
Support:
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Speaker

Demo Video

Description:

How to visualize tens of thousands of SARS-CoV-2 analysis results? Learn about the Viral Beacon project’s solution!
Length: 24 minutes
Captions: Assunta DeSanto
Created: 8 December 2021
Materials:
Support:
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Speaker

Genome annotation

Lecture Video

Description:

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
Length: 3 minutes
Captions: Anthony Bretaudeau
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Load genome into Galaxy
  • Annotate genome with Prokka
  • View annotations in JBrowse
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Speaker

Tutorial Video

Description:

In this tutorial we will use Prokka to annotate a draft genome sequence. Prokka finds and annotates features (both protein coding regions and RNA genes, i.e. tRNA, rRNA) present on on a sequence. Prokka can be used to annotate bacterial, archaeal and viral genomes quickly, generating standard output files in GenBank, EMBL and gff formats.”
Length: 20 minutes
Captions: Anthony Bretaudeau
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Load genome into Galaxy
  • Annotate genome with Prokka
  • View annotations in JBrowse
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Speaker

Lecture Video

Description:

This lecture gives a quick overview of Apollo
Length: 5 minutes
Captions: Anthony Bretaudeau
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Load a genome into Galaxy
  • View annotations in JBrowse
  • Learn how to load JBrowse data into Apollo
  • Learn how to manually refine genome annotations within Apollo
  • Export refined genome annotations
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Speaker

Tutorial Video

Description:

In this tutorial you will get some hands-on experience using Apollo in Galaxy
Length: 1 hour
Captions: Anthony Bretaudeau
Created: 15 February 2021
Materials:
Support:
Supported Servers: Possibly Working
Learning Objectives:
  • Load a genome into Galaxy
  • View annotations in JBrowse
  • Learn how to load JBrowse data into Apollo
  • Learn how to manually refine genome annotations within Apollo
  • Export refined genome annotations
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Speaker

Tutorial Video

Description:

Genome annotation of eukaryotes is a little more complicated than for prokaryotes: eukaryotic genomes are usually larger than prokaryotes, with more genes. The sequences determining the beginning and the end of a gene are generally less conserved than the prokaryotic ones. Many genes also contain introns, and the limits of these introns (acceptor and donor sites) are not highly conserved.

In this tutorial we will use a software tool called Funannotate (Palmer and Stajich 2020) to annotate the genome sequence of a small eukaryote: Mucor mucedo (a fungal plant pathogen).
Length: 1 hour 10 minutes
Captions: Anthony Bretaudeau
Created: 12 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Load genome into Galaxy
  • Annotate genome with Funannotate
  • Perform functional annotation using EggNOG-mapper and InterProScan
  • Evaluate annotation quality with BUSCO
  • View annotations in JBrowse
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Speaker

Tutorial Video

Description:

The aim of repeat masking is to identify the location of all repeated elements along a genome sequence. Other tools (like annotation pipelines) can then take this information into account when producing their results.
Length: 18 minutes
Captions: Anthony Bretaudeau
Created: 10 May 2023
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Use Red and RepeatMasker to soft-mask a newly assembled genome
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Speaker

Lecture Video

Description:

This lecture talks about the basics of TnSeq analysis
Length: 10 minutes
Captions: Delphine Lariviere
Created: 10 March 2022
Materials:
Support:
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Speaker

Crispr

Lecture Video

Description:

This lecture will introduce the basic concepts involved in CRISPR screen analysis.
Length: 3 minutes
Captions: Maria Doyle
Created: 10 March 2022
Materials:
Support:
Learning Objectives:
  • Apply appropriate analysis and quality control steps for CRISPR screen data
  • Identify differentially enriched genes across conditions
  • Generate volcano plot to visualise results
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Speaker

Tutorial Video

Description:

This tutorial will walk you through a CRISPR screen analysis.
Length: 45 minutes
Captions: Maria Doyle
Created: 10 March 2022
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Apply appropriate analysis and quality control steps for CRISPR screen data
  • Identify differentially enriched genes across conditions
  • Generate volcano plot to visualise results
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Speaker

Introduction

Tutorial Video

Description:

This tutorial will introduce you to Galaxy. You will familiarize yourself with tools, workflows and histories. Those skills will be needed the next days
Length: 13 minutes
Captions: Saskia Hiltemann
Created: 21 July 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Familiarize yourself with the basics of Galaxy
  • Learn how to obtain data from external sources
  • Learn how to run tools
  • Learn how histories work
  • Learn how to create a workflow
  • Learn how to share your work
Go to the video page to see all versions.

Speaker

Demo Video

Description:

In this demo video, we will show how to perform an NGS data analysis, using a SARS-CoV-2 example dataset. If you would like to run the full tutorial yourself, please find the link below (duration 1h-1.5h).
Length: 15 minutes
Captions: Anton Nekrutenko
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
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Speaker

Variant analysis

Demo Video

Description:

A demo of SARS-CoV-2 sequencing data analysis from sequenced reads in NCBI’s SRA to called and annotated mutations for a batch of viral samples.
Length: 15 minutes
Captions: Anton Nekrutenko
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
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Speaker

Lecture Video

Length: 12 minutes
Captions: Wolfgang Maier
Created: 4 May 2023
Support:
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Speaker

Tutorial Video

Length: 55 minutes
Captions: Wolfgang Maier
Created: 10 May 2023
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Discover and obtain recommended Galaxy workflows for SARS-CoV-2 sequence data analysis through public workflow registries
  • Choose and run a workflow to discover mutations in a batch of viral samples from sequencing data obtained through a range of different protocols and platforms
  • Run a workflow to summarize and visualize the mutation discovery results for a batch of samples
  • Run a workflow to construct viral consensus sequences for the samples in a batch
  • Know different SARS-CoV-2 lineage classification systems, and use pangolin and Nextclade to assign samples to predefined lineages
  • Combine information from different analysis steps to be able to draw appropriate conclusions about individual samples and batches of viral data
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Speaker

Lecture Video

Description:

Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, in 2018 there were 10.0 million new cases of TB worldwide and 1.4 million deaths due to the disease, making TB the world’s most deadly infectious disease.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:

Variation in the genome of M. tuberculosis (Mtb) is associated with changes in phenotype, for example drug resistance and virulence. It is also useful for outbreak investigation as the single nucleotide polymorphisms (SNPs) in a sample can be used to build a phylogeny.
Length: 40 minutes
Captions: Peter van Heusden, Nadia Goué, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • How should we filter those variants
  • How can we predict drug resistance from those variants
  • How do we annotate those variants
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Speaker

Tutorial Video

Description:

To discover causal mutations of inherited diseases it’s common practice to do a trio analysis. In a trio analysis DNA is sequenced of both the patient and parents. Using this method, it’s possible to identify multiple inheritance patterns.
Length: 40 minutes
Captions: Jasper Ouwerkerk
Created: 12 May 2023
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Requesting DAC access and importing data from the EGA.
  • Pre-process VCFs using regular expressions.
  • Use annotations and phenotype information to find the causative variant(s).
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Speaker

Materials science

Video

Length: 22 minutes
Captions: Leandro Liborio
Created: 26 January 2024
Materials:
Support:
Supported Servers: Known Working
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Speaker

Metagenomics

Lecture Video

Description:

Nanopore Sequencing has many applications in a clinical setting. In this lecture, Astrid Heikema discusses how her group at the Erasmus Medical Center uses Nanopore for sequencing of bacterial Genomes.
Length: 30 minutes
Captions: Helena Rasche
Created: 15 February 2021
Support:
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Speaker

Lecture Video

Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.
Length: 15 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:

Metatranscriptomics analysis examines how the microbiome responds to the environment by studying the taxonomic composition and functional analysis of genes expressed by the microbiome, using microbial community RNASeq data and subsequent metatranscriptomics workflows. This workshop will introduce researchers to the basic concepts and tools from the ASaiM-MT workflow. ASaiM-MT provides a curated collection of tools to explore and visualize taxonomic and functional information from metatranscriptomic sequences.
Length: 1 hour 5 minutes
Captions: Paul Zierep
Created: 17 May 2023
Materials:
Support:
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Speaker

Video

Length: 1 hour 15 minutes
Captions: Sophia Hampe
Created: 16 May 2023
Materials:
Support:
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Speaker

Tutorial Video

Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.
Length: 1 hour 37 minutes
Captions: Saskia Hiltemann
Created: 19 May 2023
Materials:
Support:
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Speaker

Tutorial Video

Description:

This tutorial will guide you through the process of assembling your Nanopore-sequenced bacterial samples and determining the presence of antibiotic resistance genes.
Length: 45 minutes
Captions: Bérénice Batut
Created: 15 February 2021
Materials:
Support:
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Speaker

Video

Description:

In this tutorial, we will be presenting a series of Galaxy workflows whose main goals are 1) to agnostically detect pathogens (What exactly is this pathogen and what virulence factors does it carry?) from data extracted directly (without prior cultivation) from a potentially contaminated sample (e.g. food like chicken, beef, etc.) and sequenced using Nanopore, and 2) to compare different samples to trace the possible source of contamination
Length: 1 hour 45 minutes
Captions: Engy Nasr
Created: 1 May 2023
Materials:
Support:
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Speaker

Tutorial Video

Length: 1 hour 5 minutes
Captions: Sophia Hampe
Created: 10 May 2023
Materials:
Support:
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Speaker

Video

Description:

In this tutorial, we will learn how to run metagenomic assembly tool and evaluate the quality of the generated assemblies. To do that, we will use data from the study: Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem. For an in-depth analysis of the structure and functions of the coffee microbiome, a temporal shotgun metagenomic study (six time points) was performed. The six samples have been sequenced with Illumina MiSeq utilizing whole genome sequencing.
Length: 1 hour
Captions: Bérénice Batut, Sophia Hampe
Created: 2 May 2023
Materials:
Support:
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Speaker

Proteogenomics

Lecture Video

Description:

In this opening presentation, the basic components of proteogenomics are described, including the main steps in the bioinformatics analysis workflow that make up this approach and will be detailed in the following tutorials. Some examples of research questions that benefit from a proteogenomics approach are also highlighted.
Length: 20 minutes
Captions: Emma Leith
Created: 15 February 2021
Materials:
Support:
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Speaker

Proteomics

Lecture Video

Description:

This lecture will introduce EncyclopeDIA.
Length: 20 minutes
Captions: Emma Leith
Created: 25 June 2021
Materials:
Support:
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Speakers

Tutorial Video

Description:

This tutorial will walk you through an analysis with EncyclopeDIA step by step.
Length: 30 minutes
Captions: Mehmet Tekman
Created: 25 June 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Understand the difference between DDA and DIA methods
  • Performing quantitative analysis using DIA data
  • Understand the purpose and benefits of using a Chromatogram Library for detection of peptides
  • You can use Bloom's Taxonomy to write effective learning objectives
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Speaker

Lecture Video

Description:

This lecture will provide an introduction to mass spectrometry (MS) based proteomics analysis. Slides created by Melanie Föll.
Length: 20 minutes
Captions: Melanie Föll
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
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Speaker

Tutorial Video

Description:

Modern mass spectrometry-based proteomics enables the identification and quantification of thousands of proteins. Therefore, quantitative mass spectrometry represents an indispensable technology for biological and clinical research. Statistical analyses are required for the unbiased answering of scientific questions and to uncover all important information in the proteomic data. In this training we will cover the full analysis workflow from label-free, data dependent acquisition (DDA) raw data to statistical results. We’ll use two popular quantitative proteomics software: MaxQuant and MSstats.
Length: 1 hour
Captions: Melanie Föll
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Learn how to use MaxQuant and MSstats for the analysis of label-free shotgun (DDA) data
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Speaker

Demo Video

Description:

In this tutorial, the basic workflow for metaproteomics is described, which includes database search, seeking taxonomy information and functional analysis. Related metaproteomics and functional microbiome tools and GTN tutorials are also mentioned in this tutorial.
Length: 1 hour
Captions: Emma Leith
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • A taxonomy and functional analysis of metaproteomic mass spectrometry data.
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Speaker

Lecture & Demo Video

Description:

The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world’s population. Accurate and timely diagnosis of COVID-19 infection is an important step for providing care and containing its further spread. In this tutorial, attendees will be introduced to two workflows – a) database search workflow and b) peptide validation workflow. Attendees of the workshop will get an in-depth knowledge of the Galaxy workflows that detect SARS-CoV-2 peptides (10.1186/s12014-021-09321-1)) and co-infecting pathogen peptides (10.1021/acs.jproteome.0c00822).
Length: 35 minutes
Captions: Emma Leith
Created: 15 February 2021
Materials:
Support:
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Speakers

Tutorial Video

Description:

In this tutorial, we will provide a walkthrough on how to generate a customized protein sequence database using RNA-Seq data. The resultant FASTA database contains sequences with single amino acid variants (SAVs), insertions and deletions (indels)and transcript assemblies (splicing variants). This database can then be used to identify protein sequence variants from the mass spectrometry data.
Length: 40 minutes
Captions: Emma Leith
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Generating a customized Protein sequence database with variants, indels, splice junctions and known sequences.
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Speaker

Demo Video

Description:

In this demonstration, we’re continuing the process of proteogenomic analysis. Here, we search mass spectrometry data against a custom proteogenomics FASTA database to create peptide spectral matches (PSMs) for each dataset; we also isolate non-canonical peptides from the resulting data for further analysis. If you would like to view the results yourself, we provide example histories in the FAQ document
Length: 30 minutes
Captions: Emma Leith
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • A proteogenomic data analysis of mass spectrometry data to identify and visualize variant peptides.
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Speaker

Demo Video

Description:

In this demonstration, we will investigate the peptides that were identified during proteogenomics tutorial 2. We will identify the presence of novel proteoforms that are absent in the reference database, annotate the novel peptides and visualize them using the Multi-omics Visualization Platform (MVP). If you would like to view the results yourself, we provide example histories in the FAQ document
Length: 40 minutes
Captions: Subina Mehta
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • How to assign and visualize the genomic localization of these identified novel proteoforms?
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Speaker

Tutorial Video

Description:

This tutorial covers an annotation pipeline for a protein list identified by LC-MS/MS experiments.
Length: 30 minutes
Captions: Florence Combes
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Execute a complete annotation pipeline of a protein list identified by LC-MS/MS experiments
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Speaker

Virology

Lecture Video

Length: 12 minutes
Captions: Wolfgang Maier
Created: 4 May 2023
Support:
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Speaker

One health

Lecture Video

Length: 10 minutes
Captions: Wolfgang Maier
Created: 19 May 2023
Materials:
Support:
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Speaker

Sequence analysis

Removal of human reads from SARS-CoV-2 sequencing data

image indicating this is a self-study session. This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: Removal of human reads from SARS-CoV-2 sequencing data
Materials:
Support:
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Instructor

Lecture Video

Description:

This lecture covers the basic concepts involved in mapping sequencing reads to a reference genome.
Length: 10 minutes
Captions: Daniel Blankenberg
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • You will learn what mapping is
  • A genome browser is shown that helps you to understand your data
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Speaker

Tutorial Video

Description:

In this tutorial you will map sequencing data to a reference genome, and explore the mapped reads in a genome browser.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • You will learn what mapping is
  • A genome browser is shown that helps you to understand your data
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Speaker

Lecture Video

Description:

This lecture goes over the concepts involved in assessing the quality of your sequencing data.
Length: 40 minutes
Captions: Yvonne Hiltemann, Nadia Goué, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
  • Assess long reads FASTQ quality using Nanoplot and PycoQC
  • Perform quality correction with Cutadapt (short reads)
  • Summarise quality metrics MultiQC
  • Process single-end and paired-end data
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Speaker

Tutorial Video

Description:

In this tutorial you will get some hand-on experience performing a quality assessment on sequencing data.
Length: 50 minutes
Captions: Andrew Lonsdale
Created: 19 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
  • Assess long reads FASTQ quality using Nanoplot and PycoQC
  • Perform quality correction with Cutadapt (short reads)
  • Summarise quality metrics MultiQC
  • Process single-end and paired-end data
Go to the video page to see all versions.

Speaker

Statistics

Tutorial Video

Description:

This hands-on tutorial covers Convolutional Neural Networks (CNN)
Length: 1 hour
Captions: Filippos Zacharopoulos
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working
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Speaker

Tutorial Video

Description:

This hands-on tutorial covers Feedforward Neural Networks (FNN)
Length: 1 hour 10 minutes
Captions: Kaivan Kamali
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
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Speaker

Tutorial Video

Description:

This hands-on tutorial covers Recurrenct Neural Networks (RNN)
Length: 50 minutes
Captions: Kaivan Kamali
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
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Speaker

Tutorial Video

Description:

The talk includes a lecture followed by a hands-on session to apply multiple classification algorithms on the Quantitative structure-activity relationship (QSAR) dataset to predict the biodegradable activity of chemical compounds. QSAR models attempt to predict the activity or property of chemicals based on their chemical structure. To achieve this, a database of compounds is collected for which the property of interest is known. For each compound, molecular descriptors are collected which describe the structure (for example - molecular weight, number of nitrogen atoms, number of carbon-carbon double bonds). Using these descriptors, a model is constructed which is capable of predicting the property of interest for a new, unknown molecule. In this tutorial, we will use a database assembled from experimental data of the Japanese Ministry of International Trade and Industry to create a classification model by applying simple and complex classifiers to learn the nature of biodegradation. We will use this model to classify new molecules into one of two classes - biodegradable or non-biodegradable. Different visualisations are used to analyze the results after applying each classification algorithm. Hyperparameters of one of the classifiers are also optimised.
Length: 1 hour 50 minutes
Captions: Anup Kumar
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Learn classification background
  • Learn what a quantitative structure-analysis relationship (QSAR) model is and how it can be constructed in Galaxy
  • Learn to apply logistic regression, k-nearest neighbors, support verctor machines, random forests and bagging algorithms
  • Learn how visualizations can be used to analyze the classification results
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

The classification of fruits and vegetables offers many useful applications such as automated harvesting by robots, building up stocks for supermarkets, effective detection of specific defects, and determining fruit ripeness (Duong et al. 2020, Naranjo-Torres et al. 2020, Iswari et al. 2017). Machine Learning (ML) techniques such as Deep Learning (DL) are commonly used for image classification problems in various domains, including in agriculture (Kamilaris and Prenafeta-Boldú 2018). DL is a technique inspired by how a human brain operates. Due to the increased availability of compute capacity and training data, DL techniques have become very popular in recent years. In this tutorial, we will use Galaxy’s ML toolkit to build a DL model to classify fruit and vegetable images. Our DL model is trained and evaluated on Fruit 360 dataset (Mureşan and Oltean 2018)
Length: 1 hour
Captions: Kaivan Kamali
Created: 19 January 2022
Materials:
Support:
Supported Servers: Known Working
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Speaker

Tutorial Video

Description:

This is an Introduction to Machine Learning in R, in which you’ll learn the basics of unsupervised learning for pattern recognition and supervised learning for prediction. At the end of this workshop, we hope that you will - appreciate the importance of performing exploratory data analysis (or EDA) before starting to model your data. - understand the basics of unsupervised learning and know the examples of principal component analysis (PCA) and k-means clustering. - understand the basics of supervised learning for prediction and the differences between classification and regression. - understand modern machine learning techniques and principles, such as test train split, k-fold cross validation and regularization. - be able to write code to implement the above techniques and methodologies using R, caret and glmnet. We will not be focusing on the mathematical foundation for each of the methods and approaches we’ll be discussing. There are many resources that can provide this context, but for the purposes of this workshop we believe that they are beyond the scope.
Length: 1 hour 30 minutes
Captions: Maria Tsagiopoulou
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Understand the ML taxonomy and the commonly used machine learning algorithms for analysing -omics data
  • Understand differences between ML algorithms categories and to which kind of problem they can be applied
  • Understand different applications of ML in different -omics studies
  • Use some basic, widely used R packages for ML
  • Interpret and visualize the results obtained from ML analyses on omics datasets
  • Apply the ML techniques to analyse their own datasets
Go to the video page to see all versions.

Speaker

Lecture Video

Description:

The lecture explains introductory concepts in machine learning such as supervised and unsupervised learning, classification and regression, hyperparameter optimisation, cross-validation, train, test and validation sets.
Length: 15 minutes
Captions: Anup Kumar
Created: 15 February 2021
Materials:
Support:
Go to the video page to see all versions.

Speaker

Lecture & Tutorial Video

Description:

The talk includes a lecture followed by a hands-on session to apply multiple regression algorithms on the DNA-methylation dataset to predict biological age. In this tutorial, we will build a regression model for chronological age prediction, based on DNA methylation. This is based on the work of Jana Naue et al. 2017, in which biomarkers are examined to predict the chronological age of humans by analyzing the DNA methylation patterns. Different machine learning algorithms are used in this study to make an age prediction. It has been recognized that within each individual, the level of DNA methylation changes with age. This knowledge is used to select useful biomarkers from DNA methylation datasets. The CpG sites with the highest correlation to age are selected as the biomarkers (and therefore features for building a regression model). In this tutorial, specific biomarkers are analyzed by machine learning algorithms to create an age prediction model. Multiple visualisations are also used to analyse the predictions made by simple and complex regressors and hyperparameters of one of the regressors also optimised.
Length: 1 hour 29 minutes
Captions: Anup Kumar
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Learn regression background
  • Apply regression based machine learning algorithms
  • Learn ageing biomarkers and predict age from DNA methylation datasets
  • Learn how visualizations can be used to analyze predictions
Go to the video page to see all versions.

Speaker

Synthetic biology

Demo Video

Length: 3 minutes
Captions: Kenza Bazi-Kabbaj
Created: 11 May 2022
Materials:
Support:
Go to the video page to see all versions.

Speaker

Demo Video

Length: 5 minutes
Captions: Kenza Bazi-Kabbaj
Created: 26 September 2022
Materials:
Support:
Go to the video page to see all versions.

Speaker

Demo Video

Length: 5 minutes
Captions: Kenza Bazi-Kabbaj
Created: 23 June 2022
Materials:
Support:
Go to the video page to see all versions.

Speaker

Transcriptomics

Tutorial Video

Description:

Bulk RNA-seq data contains a mixture of transcript signatures from several types of cells. We wish to deconvolve this mixture to obtain estimates of the proportions of cell types within the bulk sample. To do this, we can use single cell RNA-seq data as a reference for estimating the cell type proportions within the bulk data.

In this tutorial, we will use bulk and single-cell RNA-seq data, including matrices of similar tissues from different sources, to illustrate how to infer cell type abundances from bulk RNA-seq.
Length: 20 minutes
Captions: Mehmet Tekman, Wendi Bacon
Created: 8 March 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Construct Bulk and scRNA Expression Set Objects
  • Inspect these objects for various properties
  • Measure the abundance of certain cell type cluster markers compared to others
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

In this tutorial, we will use de novo transcript reconstruction to infer transcript structures from aligned reads. We will identify and quantify transcripts present in two different cell state and determine which transcripts are differentially expressed between the two states.
Length: 48 minutes
Captions: Mallory Freeberg
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Analysis of RNA sequencing data using a reference genome
  • Reconstruction of transcripts without reference transcriptome (de novo)
  • Analysis of differentially expressed genes
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 15 minutes
Captions: Julia Jakiela
Created: 11 April 2023
Materials:
Support:
Supported Servers: Known Working
Go to the video page to see all versions.

Speaker

Demo Video

Description:

This tutorial will take you from raw FASTQ files to a cell x gene data matrix in AnnData format. What’s a data matrix, and what’s AnnData format? Well you’ll find out! Importantly, this is the first step in processing single cell data in order to start analysing it.
Length: 30 minutes
Captions: Wendi Bacon
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Generate a cellxgene matrix for droplet-based single cell sequencing data
  • Interpret quality control (QC) plots to make informed decisions on cell thresholds
  • Find relevant information in GTF files for the particulars of their study, and include this in data matrix metadata
Go to the video page to see all versions.

Speaker

Demo Video

Length: 11 minutes
Captions: Graeme Tyson
Created: 9 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Combine data matrices from different samples in the same experiment
  • Label the metadata for downstream processing
Go to the video page to see all versions.

Speaker

Removing the effects of the cell cycle

image indicating this is a self-study session. This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: Removing the effects of the cell cycle
Description: Single-cell RNA sequencing can be sensitive to both biological and technical variation, i which is why preparing your data carefully is an important part of the analysis. You want the results to reflect the interesting differences in expression between cells that relate to their type or state. Other sources of variation can conceal or confound this, making it harder for you to see what is going on. One common biological confounder is the cell cycle. Cells express different genes during different parts of the cell cycle, depending on whether they are in their growing phase (G1), duplicating their DNA (the S or Synthesis phase), or dividing in two (G2/M or Mitosis phase). If these cell cycle genes are having a big impact on your data, then you could end up with separate clusters that actually represent cells of the same type that are just at different stages of the cycle. In this tutorial, we will identify the genes whose expression is known to vary during the cell cycle so that we can use them to regress out (or remove) the effects of the cell cycle on the clustering.
Materials:
Support:
Learning Objectives:
  • Identify the cell cycle genes
  • Use the cell cycle genes to regress out the effects of the cell cycle
  • Create PCA plots to understand the impact of the regression
Go to the video page to see all versions.

Instructor

Lecture Video

Description:

RNA sequencing is used to assess the expression levels of genes. This video introduces the important concepts related to RNA-seq analysis.
Length: 30 minutes
Captions: Nadia Goué, Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
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Speaker

Lecture Video

Length: 10 minutes
Captions: The Global Galaxy Community
Created: 20 April 2021
Materials:
Support:
Learning Objectives:
  • Perform miRNA differential expression analysis
  • Understand the quasi-mapping-based Salmon method for quantifying the expression of transcripts using RNA-Seq data
  • Idenfity potential miRNAs involved in brassinosteroid-mediated regulation networks
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 1 hour 10 minutes
Captions: Cristóbal Gallardo
Created: 25 July 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Perform miRNA differential expression analysis
  • Understand the quasi-mapping-based Salmon method for quantifying the expression of transcripts using RNA-Seq data
  • Idenfity potential miRNAs involved in brassinosteroid-mediated regulation networks
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

In this tutorial we will walk you through the process of an RNA-seq analysis, comparing gene expression levels between different conditions and assessing impacted gene pathways.
Length: 2 hours 50 minutes
CYOA: This is a Choose-Your-Own-Adventure (CYOA) tutorial! This means you will be presented with a choice at the end of the video; pick one of the paths and a new video will play. Happy Adventuring!
Captions: Lucille Delisle
Created: 15 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Check a sequence quality report generated by FastQC for RNA-Seq data
  • Explain the principle and specificity of mapping of RNA-Seq data to an eukaryotic reference genome
  • Select and run a state of the art mapping tool for RNA-Seq data
  • Evaluate the quality of mapping results
  • Describe the process to estimate the library strandness
  • Estimate the number of reads per genes
  • Explain the count normalization to perform before sample comparison
  • Construct and run a differential gene expression analysis
  • Analyze the DESeq2 output to identify, annotate and visualize differentially expressed genes
  • Perform a gene ontology enrichment analysis
  • Perform and visualize an enrichment analysis for KEGG pathways
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

In this tutorial, we will visualize our RNA-seq analysis results using R.
Length: 30 minutes
Captions: Helena Rasche, Saskia Hiltemann, Fotis E. Psomopoulos
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Describe the role of data, aesthetics, geoms, and layers in `ggplot` functions.
  • Customize plot scales, titles, subtitles, themes, fonts, layout, and orientation.
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

The previous tutorial introduced volcano plots and showed how they can be generated with the Galaxy Volcano plot tool. In this tutorial we show how you can customise a plot using the R script output from the tool.
Length: 15 minutes
Captions: Maria Doyle
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Learn how to use R to edit Volcano plot colours, points, labels and categories
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

This tutorial will show you how you can create volcano plots from your RNA-Seq analysis results using Galaxy tools.
Length: 10 minutes
Captions: Maria Doyle
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Create a volcano plot of RNA-seq data to visualize significant genes
Go to the video page to see all versions.

Speaker

Demo Video

Description:

You’ve done all the hard work of preparing a single cell matrix, processing it, plotting it, interpreting it, finding lots of lovely genes, all within the glorious Galaxy interface. Now you want to infer trajectories, or relationships between cells… and you’ve been threatened with learning Python to do so! Well, fear not. If you can have a run-through of a basic python coding introduction, then that will help you make more sense of this tutorial, however you’ll be able to make and interpret glorious plots even without understanding the Python coding language. This is the beauty of Galaxy - all the ‘set-up’ is identical across computers, because it’s browser based. So fear not!
Length: 10 minutes
Captions: Wendi Bacon
Created: 15 February 2021
Materials:
Support:
Supported Servers: Possibly Working
Learning Objectives:
  • Execute multiple plotting methods designed to maintain lineage relationships between cells
  • Interpret these plots
Go to the video page to see all versions.

Speaker

Lecture Video

Description:

Single-cell RNA-seq analysis is a rapidly evolving field at the forefront of transcriptomic research, used in high-throughput developmental studies and rare transcript studies to examine cell heterogeneity within a populations of cells. The cellular resolution and genome wide scope make it possible to draw new conclusions that are not otherwise possible with bulk RNA-seq. Slides created by Mehmet Tekman.
Length: 20 minutes
Captions: Mehmet Tekman
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • To understand the pitfalls in scRNA-seq sequencing and amplification, and how they are overcome.
  • Know the types of variation in an analysis and how to control for them.
  • Grasp what dimension reduction is, and how it might be performed.
  • Be familiarised with the main types of clustering techniques and when to use them.
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

This tutorial replicates the paper “Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing” (Denyer et al. 2019), where the major plant cell types are recovered in the data as well as distinguishing between QC and meristematic cells. The original paper used the Seurat analysis suite (Satija et al. 2015), but here we will use the ScanPy analysis suite (Wolf et al. 2018) integrated within the single-cell resources in Galaxy (Tekman et al. 2020).
Length: 55 minutes
Captions: Mehmet Tekman
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Perform filtering, dimensionality reduction, and clustering
  • Generate a DotPlot emulating the original paper using a different analysis tool
  • Determine robust clusters across scRNA-seq pipelines
Go to the video page to see all versions.

Speaker

Demo Video

Description:

10x genomics has provided not only a cost-effective high-throughput solution to understanding sample heterogeneity at the individual cell level, but has defined the standards of the field that many downstream analysis packages are now scrambling to accommodate. Please work through the full tutorial yourself to get all the details.
Length: 19 minutes
Captions: Pavankumar Videm
Created: 19 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Demultiplex single-cell FASTQ data from 10X Genomics
  • Learn about transparent matrix formats
  • Understand the importance of high and low quality cells
Go to the video page to see all versions.

Speaker

Demo Video

Description:

In this tutorial, we will investigate clustering of single-cell data from 10x Genomics, including preprocessing, clustering and the identification of cell types via known marker genes, using Scanpy. It will be illustrated using a dataset of Peripheral Blood Mononuclear Cells (PBMC), containing 2,700 single cells. Please work through the full tutorial yourself to get all the details.
Length: 45 minutes
Captions: Hans-Rudolf Hotz
Created: 18 March 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Describe an AnnData object to store single-cell data
  • Explain the preprocessing steps for single-cell data
  • Evaluate quality of single-cell data and apply steps to select and filter cells and genes based on QC
  • Execute data normalization and scaling
  • Identify highly variable genes
  • Construct and run a dimensionality reduction using Principal Component Analysis
  • Perform a graph-based clustering for cells
  • Identify marker genes for the clusters
  • Construct and run a cell type annotation for the clusters
Go to the video page to see all versions.

Speaker

Demo Video

Description:

You’ve done all the work to make a single cell matrix, with gene counts and mitochondrial counts and buckets of cell metadata from all your variables of interest, now it’s time to fully process our data, to remove low quality cells, to reduce the many dimensions of data that make it difficult to work with, and ultimately to try to define our clusters and to find our biological meaning and insights!
Length: 30 minutes
Captions: Wendi Bacon
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Interpret quality control plots to direct parameter decisions
  • Repeat analysis from matrix to clustering
  • Identify decision-making points
  • Appraise data outputs and decisions
  • Explain why single cell analysis is an iterative (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly) process
Go to the video page to see all versions.

Speaker

Demo Video

Description:

This tutorial demonstrates the what barcodes in your sequencing data are, and how to handle them during analysis. Please work through the full tutorial yourself to get all the details.
Length: 10 minutes
Captions: Alireza Khanteymoori
Created: 18 March 2021
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Demultiplex FASTQ data via UMI-tools
  • Understand and validate the extraction of barcodes
Go to the video page to see all versions.

Speaker

Single cell

Tutorial Video

Description:

Bulk RNA-seq data contains a mixture of transcript signatures from several types of cells. We wish to deconvolve this mixture to obtain estimates of the proportions of cell types within the bulk sample. To do this, we can use single cell RNA-seq data as a reference for estimating the cell type proportions within the bulk data.

In this tutorial, we will use bulk and single-cell RNA-seq data, including matrices of similar tissues from different sources, to illustrate how to infer cell type abundances from bulk RNA-seq.
Length: 20 minutes
Captions: Mehmet Tekman, Wendi Bacon
Created: 8 March 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Construct Bulk and scRNA Expression Set Objects
  • Inspect these objects for various properties
  • Measure the abundance of certain cell type cluster markers compared to others
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 15 minutes
Captions: Julia Jakiela
Created: 11 April 2023
Materials:
Support:
Supported Servers: Known Working
Go to the video page to see all versions.

Speaker

Demo Video

Description:

This tutorial will take you from raw FASTQ files to a cell x gene data matrix in AnnData format. What’s a data matrix, and what’s AnnData format? Well you’ll find out! Importantly, this is the first step in processing single cell data in order to start analysing it.
Length: 30 minutes
Captions: Wendi Bacon
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Generate a cellxgene matrix for droplet-based single cell sequencing data
  • Interpret quality control (QC) plots to make informed decisions on cell thresholds
  • Find relevant information in GTF files for the particulars of their study, and include this in data matrix metadata
Go to the video page to see all versions.

Speaker

Demo Video

Length: 11 minutes
Captions: Graeme Tyson
Created: 9 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Combine data matrices from different samples in the same experiment
  • Label the metadata for downstream processing
Go to the video page to see all versions.

Speaker

Removing the effects of the cell cycle

image indicating this is a self-study session. This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: Removing the effects of the cell cycle
Description: Single-cell RNA sequencing can be sensitive to both biological and technical variation, i which is why preparing your data carefully is an important part of the analysis. You want the results to reflect the interesting differences in expression between cells that relate to their type or state. Other sources of variation can conceal or confound this, making it harder for you to see what is going on. One common biological confounder is the cell cycle. Cells express different genes during different parts of the cell cycle, depending on whether they are in their growing phase (G1), duplicating their DNA (the S or Synthesis phase), or dividing in two (G2/M or Mitosis phase). If these cell cycle genes are having a big impact on your data, then you could end up with separate clusters that actually represent cells of the same type that are just at different stages of the cycle. In this tutorial, we will identify the genes whose expression is known to vary during the cell cycle so that we can use them to regress out (or remove) the effects of the cell cycle on the clustering.
Materials:
Support:
Learning Objectives:
  • Identify the cell cycle genes
  • Use the cell cycle genes to regress out the effects of the cell cycle
  • Create PCA plots to understand the impact of the regression
Go to the video page to see all versions.

Instructor

Demo Video

Description:

You’ve done all the hard work of preparing a single cell matrix, processing it, plotting it, interpreting it, finding lots of lovely genes, all within the glorious Galaxy interface. Now you want to infer trajectories, or relationships between cells… and you’ve been threatened with learning Python to do so! Well, fear not. If you can have a run-through of a basic python coding introduction, then that will help you make more sense of this tutorial, however you’ll be able to make and interpret glorious plots even without understanding the Python coding language. This is the beauty of Galaxy - all the ‘set-up’ is identical across computers, because it’s browser based. So fear not!
Length: 10 minutes
Captions: Wendi Bacon
Created: 15 February 2021
Materials:
Support:
Supported Servers: Possibly Working
Learning Objectives:
  • Execute multiple plotting methods designed to maintain lineage relationships between cells
  • Interpret these plots
Go to the video page to see all versions.

Speaker

Lecture Video

Description:

Single-cell RNA-seq analysis is a rapidly evolving field at the forefront of transcriptomic research, used in high-throughput developmental studies and rare transcript studies to examine cell heterogeneity within a populations of cells. The cellular resolution and genome wide scope make it possible to draw new conclusions that are not otherwise possible with bulk RNA-seq. Slides created by Mehmet Tekman.
Length: 20 minutes
Captions: Mehmet Tekman
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • To understand the pitfalls in scRNA-seq sequencing and amplification, and how they are overcome.
  • Know the types of variation in an analysis and how to control for them.
  • Grasp what dimension reduction is, and how it might be performed.
  • Be familiarised with the main types of clustering techniques and when to use them.
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

This tutorial replicates the paper “Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing” (Denyer et al. 2019), where the major plant cell types are recovered in the data as well as distinguishing between QC and meristematic cells. The original paper used the Seurat analysis suite (Satija et al. 2015), but here we will use the ScanPy analysis suite (Wolf et al. 2018) integrated within the single-cell resources in Galaxy (Tekman et al. 2020).
Length: 55 minutes
Captions: Mehmet Tekman
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Perform filtering, dimensionality reduction, and clustering
  • Generate a DotPlot emulating the original paper using a different analysis tool
  • Determine robust clusters across scRNA-seq pipelines
Go to the video page to see all versions.

Speaker

Demo Video

Description:

10x genomics has provided not only a cost-effective high-throughput solution to understanding sample heterogeneity at the individual cell level, but has defined the standards of the field that many downstream analysis packages are now scrambling to accommodate. Please work through the full tutorial yourself to get all the details.
Length: 19 minutes
Captions: Pavankumar Videm
Created: 19 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Demultiplex single-cell FASTQ data from 10X Genomics
  • Learn about transparent matrix formats
  • Understand the importance of high and low quality cells
Go to the video page to see all versions.

Speaker

Demo Video

Description:

In this tutorial, we will investigate clustering of single-cell data from 10x Genomics, including preprocessing, clustering and the identification of cell types via known marker genes, using Scanpy. It will be illustrated using a dataset of Peripheral Blood Mononuclear Cells (PBMC), containing 2,700 single cells. Please work through the full tutorial yourself to get all the details.
Length: 45 minutes
Captions: Hans-Rudolf Hotz
Created: 18 March 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Describe an AnnData object to store single-cell data
  • Explain the preprocessing steps for single-cell data
  • Evaluate quality of single-cell data and apply steps to select and filter cells and genes based on QC
  • Execute data normalization and scaling
  • Identify highly variable genes
  • Construct and run a dimensionality reduction using Principal Component Analysis
  • Perform a graph-based clustering for cells
  • Identify marker genes for the clusters
  • Construct and run a cell type annotation for the clusters
Go to the video page to see all versions.

Speaker

Demo Video

Description:

You’ve done all the work to make a single cell matrix, with gene counts and mitochondrial counts and buckets of cell metadata from all your variables of interest, now it’s time to fully process our data, to remove low quality cells, to reduce the many dimensions of data that make it difficult to work with, and ultimately to try to define our clusters and to find our biological meaning and insights!
Length: 30 minutes
Captions: Wendi Bacon
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Interpret quality control plots to direct parameter decisions
  • Repeat analysis from matrix to clustering
  • Identify decision-making points
  • Appraise data outputs and decisions
  • Explain why single cell analysis is an iterative (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly) process
Go to the video page to see all versions.

Speaker

Visualisation

Tutorial Video

Description:

The previous tutorial introduced volcano plots and showed how they can be generated with the Galaxy Volcano plot tool. In this tutorial we show how you can customise a plot using the R script output from the tool.
Length: 15 minutes
Captions: Maria Doyle
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Learn how to use R to edit Volcano plot colours, points, labels and categories
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

This tutorial will show you how you can create volcano plots from your RNA-Seq analysis results using Galaxy tools.
Length: 10 minutes
Captions: Maria Doyle
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Create a volcano plot of RNA-seq data to visualize significant genes
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Speaker

Lecture Video

Description:

Circos is a popular tool for creating circular graphs to display genomic data. This video will introduce this tool and how to use it within Galaxy
Length: 6 minutes
Captions: Assunta DeSanto, Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Create a number of Circos plots using the Galaxy tool
  • Familiarise yourself with the various different track types
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Speaker

Tutorial Video

Description:

Circos is a popular tool for creating circular graphs to display genomic data. This video will introduce this tool and how to use it within Galaxy
Length: 50 minutes
Captions: Beatriz Serrano-Solano, Helena Rasche, Saskia Hiltemann, Alireza Khanteymoori
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Create a number of Circos plots using the Galaxy tool
  • Familiarise yourself with the various different track types
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Speaker

Tuberculosis

Tutorial Video

Description:

Variation in the genome of M. tuberculosis (Mtb) is associated with changes in phenotype, for example drug resistance and virulence. It is also useful for outbreak investigation as the single nucleotide polymorphisms (SNPs) in a sample can be used to build a phylogeny.
Length: 40 minutes
Captions: Peter van Heusden, Nadia Goué, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • How should we filter those variants
  • How can we predict drug resistance from those variants
  • How do we annotate those variants
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Speaker

Webinar Video

Description:

Principles of drug resistance detection from genomic data
Length: 20 minutes
Captions: This is a non-GTN video, we cannot guarantee captions
Created: 1 January 2023
Support:
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Speaker

Webinar Video

Description:

Main aspects of clustering analysis to infer transmission in MTBC
Length: 15 minutes
Captions: This is a non-GTN video, we cannot guarantee captions
Created: 1 January 2023
Support:
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Speaker

Webinar Video

Description:

This video will introduce one special type of mutations to take into account when studying drug resistance patterns
Length: 15 minutes
Captions: This is a non-GTN video, we cannot guarantee captions
Created: 1 January 2023
Support:
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Speaker

Webinar Video

Description:

Clustering as an approximation to infer transmission
Length: 15 minutes
Captions: This is a non-GTN video, we cannot guarantee captions
Created: 1 January 2023
Support:
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Speaker

Webinar

Webinar Video

Length: 1 hour 5 minutes
Captions: The Global Galaxy Community
Created: 12 May 2021
Materials:
Support:
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Speakers

Webinar Video

Length: 1 hour 10 minutes
Captions: Saskia Hiltemann
Created: 28 April 2021
Materials:
Support:
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Speakers

Webinar Video

Description:

Wondering how to get started, or how to do a particular type of analysis, or how to scale to thousands of datasets? This webinar will highlight how to find the resources and help you need for each of these questions and more.
Length: 1 hour 10 minutes
Captions: Saskia Hiltemann
Created: 21 April 2021
Materials:
Support:
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Speaker

Webinar Video

Length: 59 minutes
Captions: Helena Rasche
Created: 26 May 2021
Materials:
Support:
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Speakers

Wetlab

Demo Video

Description:

This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Support:
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Speaker

Ro crate

Tutorial Video

Length: 17 minutes
Captions: Stian Soiland-Reyes
Created: 14 April 2023
Materials:
Support:
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Speaker

Publishing My First™ RO-Crate

RO Crate logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: Publishing My First™ RO-Crate
Materials:
Support:
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Instructor

RO-Crate in Python

RO Crate logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: RO-Crate in Python
Materials:
Support:
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Instructor

Workflow Run RO-Crate Introduction

RO Crate logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: Workflow Run RO-Crate Introduction
Materials:
Support:
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Instructor

Tutorial Video

Length: 35 minutes
Captions: Australian Biocommons
Created: 21 March 2023
Materials:
Support:
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Speaker

Best practices for workflows in GitHub repositories

RO Crate logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: Best practices for workflows in GitHub repositories
Materials:
Support:
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Instructor

Submitting workflows to LifeMonitor

RO Crate logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: Submitting workflows to LifeMonitor
Materials:
Support:
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Instructor

Python

RO-Crate in Python

RO Crate logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: RO-Crate in Python
Materials:
Support:
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Instructor

Workflowhub

Tutorial Video

Length: 35 minutes
Captions: Australian Biocommons
Created: 21 March 2023
Materials:
Support:
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Speaker

Bioconductor

Demo Video

Description:

This video will help you get setup on the BioConductor Galaxy to run the tutorials in this module.
Length: 5 minutes
Captions: Bioconductor
Created: 5 May 2023
Materials:
Support:
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Speaker

Introduction to data analysis with R and Bioconductor

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: Introduction to data analysis with R and Bioconductor
Description: The Data science lesson is based on the Carpentries Ecology Curriculum. There are no pre-requisites for this module, and the materials assume no prior knowledge about R and Bioconductor. It introduces R, RStudio, teaches data cleaning, management, analysis, and visualisation and introduces some Bioconductor concepts.
Materials:
Support:
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Instructor

The Bioconductor project

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: The Bioconductor project
Description: The Bioconductor project lesson provides an introduction to the Bioconductor project such as the Bioconductor home page, packages, package landing pages, and package vignettes, where to find help, Bioconductor workflows, Bioconductor release schedule and versions, some core infrastructure,.. It is meant to be use in combination with other modules as part of a wider workshop.
Materials:
Support:
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Instructor

R for Mass Spectrometry

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: R for Mass Spectrometry
Description: This material introduces participants to the analysis and exploration of mass spectrometry (MS) based proteomics data using R and Bioconductor. The course will cover all levels of MS data, from raw data to identification and quantitation data, up to the statistical interpretation of a typical shotgun MS experiment and will focus on hands-on tutorials. At the end of this course, the participants will be able to manipulate MS data in R and use existing packages for their exploratory and statistical proteomics data analysis.
Materials:
Support:
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Instructor

Tutorial Video

Description:

This workshop demonstrates the use of the iSEE package to create and configure interactive applications for the exploration of various types of genomics data sets (e.g., bulk and single-cell RNA-seq, CyTOF, gene expression microarray). This workshop is presented as a lab session that combines an instructor-led live demo, followed by hands-on experimentation guided by completely worked examples and stand-alone notes that participants may continue to use after the workshop.

The instructor-led live demo comprises three parts:

  1. Brief lecture on the package concept and functionality
  2. Overview of the graphical user interface
  3. Instructions to preconfigure iSEE apps

The hands-on lab comprises three parts:

  1. Inspection of single-cell RNA-seq data at various steps of a typical computational workflow, including quality control and dimensionality reduction
  2. Addition of custom panels to the user interface for advanced visualization.
  3. Additional questions from the participants, including individual use cases and suggestions for future developments
Length: 55 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 28 July 2020
Materials:
Support:
Go to the video page to see all versions.

Speakers

Tutorial Video

Description:

Concepts of causal inference in epidemiology have important ramifications for studies across bioinformatics and other fields of health research. In this workshop, we introduce basic concepts of epidemiology, study design, and causal inference for bioinformaticians. Emphasis is placed on addressing bias and confounding as common threats to assessing a causal pathway in a variety of study design types and when using common forms of analyses such as GWAS and survival analysis. Workshop participants will have the opportunity to create their own structural causal models (DAGs) using dagitty and ggdag and then use this model to determine how to assess an estimated causal effect. Examples using DESeq2, edgeR, and limma will be used to show how multivariable models can be fitted depending on the hypothesized causal relationship. Presented successfully at BioC2021 to a large audience of more than 100, updates that material by revising current examples based on participant feedback as well as content updates.
Length: 83 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 27 July 2022
Materials:
Support:
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

This tutorial will showcase analysis of single-cell RNA sequencing data following the tidy data paradigm. The tidy data paradigm provides a standard way to organise data values within a dataset, where each variable is a column, each observation is a row, and data is manipulated using an easy-to-understand vocabulary. Most importantly, the data structure remains consistent across manipulation and analysis functions.

This can be achieved with the integration of packages present in the R CRAN and Bioconductor ecosystem, including tidySingleCellExperiment and tidyverse. These packages are part of the tidytranscriptomics suite that introduces a tidy approach to RNA sequencing data representation and analysis. For more information see the tidy transcriptomics blog.
Length: 1 hour 27 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 28 July 2022
Materials:
Support:
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

This workshop consists of a demonstration of using DECIPHER and SynExtend for common analyses in comparative genomics. The immediate goal of this session is to use sequence data to uncover networks of functionally associated genes. These networks consist of genetic regions under shared evolutionary pressure, which have previously been shown to imply some degree of conserved function.
Length: 1 hour 5 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 29 July 2022
Materials:
Support:
Go to the video page to see all versions.

Speaker

SpatialOmicsOverlay Workshop

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: SpatialOmicsOverlay Workshop
Description: This workshop will introduce users to the NanoString R package SpatialOmicsOverlay. This package is designed for use in interpretation and presentation of the multi-form data generated by NanoString's GeoMx ® Digital Spatial Profiler spatial biology platform. The GeoMx DSP produces both rich imaging and genomics data. Integrating these data types facilitates a deep understanding of the profiled tissue. The SpatialOmicsOverlay package integrates both of these data types, thereby by maintaining the relationship between underlying tissue morphology and resultant gene expression. Specifically, SpatialOmicsOverlay was developed to visualize and analyze the free-handed nature of Region of Interest (ROI) selection in a GeoMx experiment, as well as the immunofluorescence-guided segmentation process. The overlay from the instrument is recreated in the R environment, which allows for plotting overlays with data like ROI type or gene expression. The package provides a convenient workflow for users to generate customized, sharable visualizations. The Introduction to SpatialOmicsOverlay vignette demonstrates how to use OME-TIFF files, which are exported from the GeoMx platform. Participants will learn how to interact with this file type and generate informative plots over images. This vignette utilizes data from our Spatial Organ Atlas. The Spatial Organ Atlas is a freely-accesible resource of whole transcriptome spatial profiles of functional components of tissues from human and mouse generated using our Whole Transcriptome Atlas RNA assay. In particular, vignette users will be analyzing data from the mouse brain. This content is similar to the vignette available with the package upon installation.
Materials:
Support:
Go to the video page to see all versions.

Instructors

fluentGenomics: A plyranges and tximeta workflow

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: fluentGenomics: A plyranges and tximeta workflow
Description: An extended workflow using the plyranges and tximeta packages for fluent genomic data analysis. Use tximeta to correctly import RNA-seq transcript quantifications and summarize them to gene counts for downstream analysis. Use plyranges for clearly expressing operations over genomic coordinates and to combine results from differential expression and differential accessibility analyses.
Materials:
Support:
Go to the video page to see all versions.

Instructor

MungeSumstats: Standardise the format of GWAS summary statistics

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: MungeSumstats: Standardise the format of GWAS summary statistics
Description: The package is designed to handle the lack of standardisation of output files by the GWAS community. The MRC IEU Open GWAS team have provided full summary statistics for >10k GWAS, which are API-accessible via the ieugwasr and gwasvcf packages. But these GWAS are only standardised in the sense that they are VCF format, and can be fully standardised with MungeSumstats. MungeSumstats provides a framework to standardise the format for any GWAS summary statistics, including those in VCF format, enabling downstream integration and analysis. It addresses the most common discrepancies across summary statistic files, and offers a range of adjustable Quality Control (QC) steps.
Materials:
Support:
Go to the video page to see all versions.

Instructor

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
Description: The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with counts summarised at the gene-level, a typical analysis involves pre-processing, exploratory data analysis, differential expression testing and pathway analysis with the results obtained informing future experiments and validation studies. In this workflow article, we analyse RNA-sequencing data from the mouse mammary gland, demonstrating use of the popular edgeR package to import, organise, filter and normalise the data, followed by the limma package with its voom method, linear modelling and empirical Bayes moderation to assess differential expression and perform gene set testing. This pipeline is further enhanced by the Glimma package which enables interactive exploration of the results so that individual samples and genes can be examined by the user. The complete analysis offered by these three packages highlights the ease with which researchers can turn the raw counts from an RNA-sequencing experiment into biological insights using Bioconductor.
Materials:
Support:
Go to the video page to see all versions.

Instructor

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
Description: RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed (DE) between two or more biological conditions. This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland. The workflow uses R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, including alignment of read sequences, data exploration, differential expression analysis, visualization and pathway analysis. Read alignment and count quantification is conducted using the Rsubread package and the statistical analyses are performed using the edgeR package. The differential expression analysis uses the quasi-likelihood functionality of edgeR.
Materials:
Support:
Go to the video page to see all versions.

Instructor

Using singscore to predict mutations in AML from transcriptomic signatures

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: Using singscore to predict mutations in AML from transcriptomic signatures
Description: Advances in RNA sequencing (RNA-seq) technologies that measure the transcriptome of biological samples have revolutionised our ability to understand transcriptional regulatory programs that underpin diseases such as cancer. We recently published singscore - a single-sample, rank-based gene set scoring method which quantifies how concordant the transcriptional profile of individual samples are relative to specific gene sets of interest. Here we demonstrate the application of singscore to investigate transcriptional profiles associated with specific mutations or genetic lesions in acute myeloid leukemia. Using matched genomic and transcriptomic data available through The Cancer Genome Atlas we show that scoring of appropriate signatures can distinguish samples with corresponding mutations, reflecting the ability of these mutations to drive aberrant transcriptional programs involved in leukemogenesis. We believe the singscore method is particularly useful for studying heterogeneity within specific subsets of cancers, and as demonstrated, singscore has the ability to identify samples where alternative mutations/genetic lesions appear to drive transcriptional programs.
Materials:
Support:
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Instructor

R

Introduction to data analysis with R and Bioconductor

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: Introduction to data analysis with R and Bioconductor
Description: The Data science lesson is based on the Carpentries Ecology Curriculum. There are no pre-requisites for this module, and the materials assume no prior knowledge about R and Bioconductor. It introduces R, RStudio, teaches data cleaning, management, analysis, and visualisation and introduces some Bioconductor concepts.
Materials:
Support:
Go to the video page to see all versions.

Instructor

The Bioconductor project

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: The Bioconductor project
Description: The Bioconductor project lesson provides an introduction to the Bioconductor project such as the Bioconductor home page, packages, package landing pages, and package vignettes, where to find help, Bioconductor workflows, Bioconductor release schedule and versions, some core infrastructure,.. It is meant to be use in combination with other modules as part of a wider workshop.
Materials:
Support:
Go to the video page to see all versions.

Instructor

R for Mass Spectrometry

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: R for Mass Spectrometry
Description: This material introduces participants to the analysis and exploration of mass spectrometry (MS) based proteomics data using R and Bioconductor. The course will cover all levels of MS data, from raw data to identification and quantitation data, up to the statistical interpretation of a typical shotgun MS experiment and will focus on hands-on tutorials. At the end of this course, the participants will be able to manipulate MS data in R and use existing packages for their exploratory and statistical proteomics data analysis.
Materials:
Support:
Go to the video page to see all versions.

Instructor

Tutorial Video

Description:

This workshop demonstrates the use of the iSEE package to create and configure interactive applications for the exploration of various types of genomics data sets (e.g., bulk and single-cell RNA-seq, CyTOF, gene expression microarray). This workshop is presented as a lab session that combines an instructor-led live demo, followed by hands-on experimentation guided by completely worked examples and stand-alone notes that participants may continue to use after the workshop.

The instructor-led live demo comprises three parts:

  1. Brief lecture on the package concept and functionality
  2. Overview of the graphical user interface
  3. Instructions to preconfigure iSEE apps

The hands-on lab comprises three parts:

  1. Inspection of single-cell RNA-seq data at various steps of a typical computational workflow, including quality control and dimensionality reduction
  2. Addition of custom panels to the user interface for advanced visualization.
  3. Additional questions from the participants, including individual use cases and suggestions for future developments
Length: 55 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 28 July 2020
Materials:
Support:
Go to the video page to see all versions.

Speakers

Tutorial Video

Description:

Concepts of causal inference in epidemiology have important ramifications for studies across bioinformatics and other fields of health research. In this workshop, we introduce basic concepts of epidemiology, study design, and causal inference for bioinformaticians. Emphasis is placed on addressing bias and confounding as common threats to assessing a causal pathway in a variety of study design types and when using common forms of analyses such as GWAS and survival analysis. Workshop participants will have the opportunity to create their own structural causal models (DAGs) using dagitty and ggdag and then use this model to determine how to assess an estimated causal effect. Examples using DESeq2, edgeR, and limma will be used to show how multivariable models can be fitted depending on the hypothesized causal relationship. Presented successfully at BioC2021 to a large audience of more than 100, updates that material by revising current examples based on participant feedback as well as content updates.
Length: 83 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 27 July 2022
Materials:
Support:
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

This tutorial will showcase analysis of single-cell RNA sequencing data following the tidy data paradigm. The tidy data paradigm provides a standard way to organise data values within a dataset, where each variable is a column, each observation is a row, and data is manipulated using an easy-to-understand vocabulary. Most importantly, the data structure remains consistent across manipulation and analysis functions.

This can be achieved with the integration of packages present in the R CRAN and Bioconductor ecosystem, including tidySingleCellExperiment and tidyverse. These packages are part of the tidytranscriptomics suite that introduces a tidy approach to RNA sequencing data representation and analysis. For more information see the tidy transcriptomics blog.
Length: 1 hour 27 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 28 July 2022
Materials:
Support:
Go to the video page to see all versions.

Speaker

Tutorial Video

Description:

This workshop consists of a demonstration of using DECIPHER and SynExtend for common analyses in comparative genomics. The immediate goal of this session is to use sequence data to uncover networks of functionally associated genes. These networks consist of genetic regions under shared evolutionary pressure, which have previously been shown to imply some degree of conserved function.
Length: 1 hour 5 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 29 July 2022
Materials:
Support:
Go to the video page to see all versions.

Speaker

SpatialOmicsOverlay Workshop

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: SpatialOmicsOverlay Workshop
Description: This workshop will introduce users to the NanoString R package SpatialOmicsOverlay. This package is designed for use in interpretation and presentation of the multi-form data generated by NanoString's GeoMx ® Digital Spatial Profiler spatial biology platform. The GeoMx DSP produces both rich imaging and genomics data. Integrating these data types facilitates a deep understanding of the profiled tissue. The SpatialOmicsOverlay package integrates both of these data types, thereby by maintaining the relationship between underlying tissue morphology and resultant gene expression. Specifically, SpatialOmicsOverlay was developed to visualize and analyze the free-handed nature of Region of Interest (ROI) selection in a GeoMx experiment, as well as the immunofluorescence-guided segmentation process. The overlay from the instrument is recreated in the R environment, which allows for plotting overlays with data like ROI type or gene expression. The package provides a convenient workflow for users to generate customized, sharable visualizations. The Introduction to SpatialOmicsOverlay vignette demonstrates how to use OME-TIFF files, which are exported from the GeoMx platform. Participants will learn how to interact with this file type and generate informative plots over images. This vignette utilizes data from our Spatial Organ Atlas. The Spatial Organ Atlas is a freely-accesible resource of whole transcriptome spatial profiles of functional components of tissues from human and mouse generated using our Whole Transcriptome Atlas RNA assay. In particular, vignette users will be analyzing data from the mouse brain. This content is similar to the vignette available with the package upon installation.
Materials:
Support:
Go to the video page to see all versions.

Instructors

fluentGenomics: A plyranges and tximeta workflow

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: fluentGenomics: A plyranges and tximeta workflow
Description: An extended workflow using the plyranges and tximeta packages for fluent genomic data analysis. Use tximeta to correctly import RNA-seq transcript quantifications and summarize them to gene counts for downstream analysis. Use plyranges for clearly expressing operations over genomic coordinates and to combine results from differential expression and differential accessibility analyses.
Materials:
Support:
Go to the video page to see all versions.

Instructor

MungeSumstats: Standardise the format of GWAS summary statistics

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: MungeSumstats: Standardise the format of GWAS summary statistics
Description: The package is designed to handle the lack of standardisation of output files by the GWAS community. The MRC IEU Open GWAS team have provided full summary statistics for >10k GWAS, which are API-accessible via the ieugwasr and gwasvcf packages. But these GWAS are only standardised in the sense that they are VCF format, and can be fully standardised with MungeSumstats. MungeSumstats provides a framework to standardise the format for any GWAS summary statistics, including those in VCF format, enabling downstream integration and analysis. It addresses the most common discrepancies across summary statistic files, and offers a range of adjustable Quality Control (QC) steps.
Materials:
Support:
Go to the video page to see all versions.

Instructor

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
Description: The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with counts summarised at the gene-level, a typical analysis involves pre-processing, exploratory data analysis, differential expression testing and pathway analysis with the results obtained informing future experiments and validation studies. In this workflow article, we analyse RNA-sequencing data from the mouse mammary gland, demonstrating use of the popular edgeR package to import, organise, filter and normalise the data, followed by the limma package with its voom method, linear modelling and empirical Bayes moderation to assess differential expression and perform gene set testing. This pipeline is further enhanced by the Glimma package which enables interactive exploration of the results so that individual samples and genes can be examined by the user. The complete analysis offered by these three packages highlights the ease with which researchers can turn the raw counts from an RNA-sequencing experiment into biological insights using Bioconductor.
Materials:
Support:
Go to the video page to see all versions.

Instructor

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline

Bioconductor logo This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
Description: RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed (DE) between two or more biological conditions. This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland. The workflow uses R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, including alignment of read sequences, data exploration, differential expression analysis, visualization and pathway analysis. Read alignment and count quantification is conducted using the Rsubread package and the statistical analyses are performed using the edgeR package. The differential expression analysis uses the quasi-likelihood functionality of edgeR.
Materials:
Support:
Go to the video page to see all versions.

Instructor

Using singscore to predict mutations in AML from transcriptomic signatures

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Tutorial: Using singscore to predict mutations in AML from transcriptomic signatures
Description: Advances in RNA sequencing (RNA-seq) technologies that measure the transcriptome of biological samples have revolutionised our ability to understand transcriptional regulatory programs that underpin diseases such as cancer. We recently published singscore - a single-sample, rank-based gene set scoring method which quantifies how concordant the transcriptional profile of individual samples are relative to specific gene sets of interest. Here we demonstrate the application of singscore to investigate transcriptional profiles associated with specific mutations or genetic lesions in acute myeloid leukemia. Using matched genomic and transcriptomic data available through The Cancer Genome Atlas we show that scoring of appropriate signatures can distinguish samples with corresponding mutations, reflecting the ability of these mutations to drive aberrant transcriptional programs involved in leukemogenesis. We believe the singscore method is particularly useful for studying heterogeneity within specific subsets of cancers, and as demonstrated, singscore has the ability to identify samples where alternative mutations/genetic lesions appear to drive transcriptional programs.
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