videos.yaml

admin/ansible-galaxy/tutorial:
  description: null
  force_archive_materials: true
  materials:
  - link: topics/admin/tutorials/ansible-galaxy/tutorial.html
    title: Tutorial (All Parts)
    type: Tutorial
  - link: topics/admin/tutorials/database/slides.html
    title: Database Slides
    type: Slides
  - link: topics/admin/tutorials/systemd-supervisor/slides.html
    title: systemd Slides
    type: Slides
  - link: topics/admin/tutorials/production/slides.html
    title: Moving Towards Production Slides
    type: Slides
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - natefoo
    - hexylena
    date: '2022-03-01'
    galaxy_version: '21.05'
    length: 2H50M
    link: LPK8rP_qUiA
    speakers:
    - natefoo
    - hexylena
  - captions:
    - natefoo
    - hexylena
    date: '2021-06-28'
    galaxy_version: '21.05'
    length: 2H47M
    link: zT70luZqPOU
    speakers:
    - natefoo
  - captions:
    - shiltemann
    - hexylena
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 53M
    link: il83uApg7Hc
    speakers:
    - hexylena
admin/ansible/slides:
  description: null
  materials:
  - link: topics/admin/tutorials/ansible/slides.html
    type: Slides
  tags:
  - admin
  type: Lecture
  versions:
  - captions:
    - martenson
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 5M
    link: KFpbfmN0OTE
    speakers:
    - jdavcs
admin/ansible/tutorial:
  description: null
  materials:
  - link: topics/admin/tutorials/ansible/tutorial.html
    type: Tutorial
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - martenson
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 61M
    link: 2KdT0sYKUeE
    speakers:
    - martenson
admin/connect-to-compute-cluster/combined:
  description: null
  materials:
  - link: topics/admin/tutorials/connect-to-compute-cluster/slides.html
    type: Slides
  - link: topics/admin/tutorials/connect-to-compute-cluster/tutorial.html
    type: Tutorial
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - cat-bro
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 31M
    link: R0NbHscL3jA
    speakers:
    - hexylena
admin/cvmfs/slides:
  description: null
  materials:
  - link: topics/admin/tutorials/cvmfs/slides.html
    type: Slides
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - galaxycommunity
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 3M
    link: g_cavAO-fBM
    speakers:
    - awspolly
admin/cvmfs/tutorial:
  description: null
  materials:
  - link: topics/admin/tutorials/cvmfs/tutorial.html
    type: Tutorial
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - slugger70
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 23M
    link: X3iFMZP_fQ8
    speakers:
    - slugger70
admin/data-library/tutorial:
  description: null
  materials:
  - link: topics/admin/tutorials/data-library/tutorial.html
    type: Tutorial
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - hexylena
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 22M
    link: 6BWu29Oiihw
    speakers:
    - shiltemann
admin/gxadmin/slides:
  description: null
  materials:
  - link: topics/admin/tutorials/gxadmin/slides.html
    type: Slides
  - link: topics/admin/tutorials/gxadmin/tutorial.html
    type: Exercise
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - galaxycommunity
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 2M
    link: QFwOgDyFSSA
    speakers:
    - awspolly
admin/interactive-tools:
  description: null
  materials:
  - link: topics/admin/tutorials/interactive-tools/slides.html
    type: Slides
  - link: topics/admin/tutorials/interactive-tools/tutorial.html
    type: Tutorial
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - abretaud
    - hexylena
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 44M
    link: lACsIhnbTbE
    speakers:
    - abretaud
admin/job-destinations/tutorial:
  description: null
  materials:
  - link: topics/admin/tutorials/job-destinations/tutorial.html
    type: Tutorial
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 31M
    link: qX8GjTJwnAk
    speakers:
    - hexylena
admin/job-metrics/tutorial:
  description: null
  materials:
  - link: topics/admin/tutorials/connect-to-compute-cluster/tutorial.html
    type: Tutorial
  tags:
  - admin
  title: Recording Job Metrics
  type: Tutorial
  versions:
  - captions:
    - beatrizserrano
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 6M
    link: 7CYI5yw9MN8
    speakers:
    - hexylena
admin/maintenance/slides:
  description: null
  materials:
  - link: topics/admin/tutorials/maintenance/slides.html
    type: Slides
  tags:
  - admin
  type: Lecture
  versions:
  - captions:
    - galaxycommunity
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 2M
    link: 41_3WHXZA-o
    speakers:
    - awspolly
admin/monitoring/slides:
  description: null
  materials:
  - link: topics/admin/tutorials/monitoring/slides.html
    type: Slides
  tags:
  - admin
  type: Lecture
  versions:
  - captions:
    - galaxycommunity
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 2M
    link: qcp9lEUxCGI
    speakers: []
admin/monitoring/tutorial:
  description: null
  materials:
  - link: topics/admin/tutorials/monitoring/tutorial.html
    type: Tutorial
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - shiltemann
    - hexylena
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 73M
    link: drUaYQtMBLY
    speakers: []
admin/object-store/exercise:
  description: null
  materials:
  - link: topics/admin/tutorials/object-store/tutorial.html
    type: Exercise
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - cat-bro
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 18M
    link: Hv2bvjk5sjE
    speakers:
    - gmauro
admin/pulsar/slides:
  description: null
  materials:
  - link: topics/admin/tutorials/pulsar/slides-plain.html
    type: Slides
  tags:
  - admin
  type: Lecture
  versions:
  - captions:
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 14M
    link: M1-Z_2tuQPI
    speakers:
    - slugger70
admin/pulsar/tutorial:
  description: null
  materials:
  - link: topics/admin/tutorials/pulsar/tutorial.html
    type: Tutorial
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - hexylena
    date: '2021-06-28'
    galaxy_version: '21.05'
    length: 1H28M
    link: f0QdF8NDhsM
    speakers:
    - slugger70
  - captions:
    - simonbray
    - slugger70
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 57M
    link: a7fKJT4Fs9k
    speakers:
    - slugger70
admin/apptainer/tutorial:
  description: Running jobs in Apptainer
  materials:
  - link: topics/admin/tutorials/apptainer/tutorial.html
    type: Tutorial
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - gallardoalba
    - slugger70
    date: '2021-06-28'
    galaxy_version: '21.05'
    length: 43M
    link: q6Dt7j713tI
    speakers:
    - slugger70
  - captions:
    - hexylena
    - cat-bro
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 16M
    link: airzg4-ETEs
    speakers:
    - hexylena
admin/tiaas/tutorial:
  description: null
  materials:
  - link: topics/admin/tutorials/tiaas/tutorial.html
    type: Tutorial
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - hexylena
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 24M
    link: tz0ZbK_8Vcc
    speakers:
    - hexylena
admin/tool-management/slides:
  description: null
  materials:
  - link: topics/admin/tutorials/tool-management/slides.html
    type: Slides
  - link: topics/admin/tutorials/tool-management/tutorial.html
    type: Tutorial
  tags:
  - admin
  type: Lecture
  versions:
  - captions:
    - cat-bro
    date: '2021-06-28'
    galaxy_version: '21.05'
    length: 17M
    link: 8Rdho_eUeKc
    speakers:
    - cat-bro
admin/tool-management/tutorial:
  description: null
  materials:
  - link: topics/admin/tutorials/tool-management/slides.html
    type: Slides
  - link: topics/admin/tutorials/tool-management/tutorial.html
    type: Tutorial
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - cat-bro
    date: '2021-06-28'
    galaxy_version: '21.05'
    length: 27M
    link: pda0v9b3vO4
    speakers:
    - cat-bro
  - captions:
    - eancelet
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 47M
    link: 7Qqwrzn--YI
    speakers:
    - cat-bro
admin/tus/tutorial:
  description: "Here you\u2019ll 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.\n"
  materials:
  - link: topics/admin/tutorials/tus/tutorial.html
    type: Tutorial
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - hexylena
    date: '2022-03-11'
    galaxy_version: '22.01'
    length: 7M
    link: v5sbIqF_0qo
    speakers:
    - hexylena
admin/upgrading/tutorial:
  description: null
  materials:
  - link: topics/admin/tutorials/upgrading/tutorial.html
    type: tutorial
  tags:
  - admin
  type: Tutorial
  versions:
  - captions:
    - slugger70
    - hexylena
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 36M
    link: OnL47MvXjoo
    speakers:
    - slugger70
admin/users-groups-quotas/slides:
  description: null
  materials:
  - link: topics/admin/tutorials/users-groups-quotas/slides.html
    type: Slides
  tags:
  - admin
  type: Lecture
  versions:
  - captions:
    - galaxycommunity
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 4M
    link: crywu31L8qg
    speakers:
    - awspolly
admin/week-overview-slides:
  description: null
  materials:
  - link: topics/admin/tutorials/ansible-galaxy/slides.html
    type: Week Overview Slides
  support_channel: admin_ansible-galaxy
  tags:
  - admin
  title: Admin Training Week Overview
  type: Tutorial
  versions:
  - captions:
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 4M
    link: JN-C5UbHthY
    speakers:
    - hexylena
admin/welcome:
  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.

    '
  materials: []
  support_channel: event-gat
  tags:
  - admin
  title: Admin Welcome
  type: Lecture
  versions:
  - captions:
    - hexylena
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 4M
    link: JN-C5UbHthY
    speakers:
    - hexylena
    - martenson
    - slugger70
    - nsoranzo
    - shiltemann
    - gmauro
    - cat-bro
assembly/assembly-with-preprocessing:
  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.
  materials:
  - link: topics/assembly/tutorials/assembly-with-preprocessing/slides.html
    type: Slides
  - link: topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html
    type: Tutorial
  tags:
  - assembly
  type: Tutorial
  versions:
  - captions:
    - mtekman
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 25M
    link: jNFLYhjgJPs
    speakers:
    - gallardoalba

assembly/largegenome/tutorial:
  description: In this tutorial, we will walk you through an assembly of a large genome, such as a plant or animal genome.
  materials:
  - link: topics/assembly/tutorials/largegenome/tutorial.html
    title: Large genome assembly and polishing
    type: Tutorial
  tags: [assembly]
  type: Tutorial
  versions:
  - link: BM70nvwWjOY
    captions: [annasyme]
    speakers:
    - annasyme
    length: 25M
    date: '2023-05-16'
    galaxy_version: '23.01'

assembly/chloroplast-assembly/tutorial:
  description: In this tutorial, you will assemble a chloroplast genome using a combination
    of short and long read data.
  materials:
  - link: topics/assembly/tutorials/chloroplast-assembly/tutorial.html
    title: Chloroplast genome assembly
    type: Tutorial
  tags:
  - assembly
  type: Lecture & Tutorial
  versions:
  - captions:
    - annasyme
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 35M
    link: eyfCyINTD_E
    speakers:
    - annasyme
assembly/general-introduction/slides:
  description: This lecture walks you through the basic concepts involved in assembling
    a genome from short-read sequencing data.
  materials:
  - link: topics/assembly/tutorials/general-introduction/slides.html
    title: An Introduction to Genome Assembly
    type: Slides
  tags:
  - assembly
  type: Lecture
  versions:
  - captions:
    - shiltemann
    - hexylena
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 25M
    link: -EX_G1griZE
    speakers:
    - slugger70
assembly/vgp_genome_assembly-workflow:
  description: 'This demo walks you through running the VGP Genome Assembly workflows,
    rather than the whole tutorial (as most GTN videos do)

    '
  materials:
  - link: topics/assembly/tutorials/vgp_genome_assembly/tutorial.html
    title: Full Tutorial (Step-by-step, not workflow-based like video)
    type: Tutorial
  - external: true
    link: https://www.dropbox.com/sh/ayix345v11n69es/AABJerasUhiD4JfSgS3g0kS7a?dl=0&preview=VGP-Gtapas-2022.pdf
    type: Non-GTN Lecture
  tags:
  - assembly
  title: Running the VGP Genome Assembly workflows
  type: Demo
  versions:
  - captions: [delphine-l]
    date: '2022-03-13'
    galaxy_version: '21.09'
    length: 10M
    link: 0EoBDiyd-84
    speakers:
    - delphine-l
climate/fates/slides:
  description: This lecture provides a brief overview of FATES
  materials:
  - link: topics/climate/tutorials/fates/slides.html
    title: Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
    type: Slides
  tags:
  - climate
  type: Lecture
  versions:
  - captions:
    - annefou
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 7M
    link: Z57C7MQG95s
    speakers:
    - awspolly
climate/fates/tutorial:
  description: This tutorial will walk you through a Galaxy analysis step by step
  materials:
  - link: topics/climate/tutorials/fates/tutorial.html
    title: Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
    type: Tutorial
  tags:
  - climate
  type: Tutorial
  versions:
  - captions:
    - s3by01
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H20M
    link: 0LsEx11eLiI
    speakers:
    - annefou
climate/pangeo-notebook/tutorial:
  description: "In this tutorial, we will learn about Xarray, one of the most used\
    \ Python\nlibrary from the Pangeo ecosystem.\n\nWe will be using data from Copernicus\
    \ Atmosphere Monitoring Service and\nmore precisely PM2.5 (Particle Matter < 2.5\
    \ \u03BCm) 4 days forecast from\nDecember, 22 2021. Parallel data analysis with\
    \ Pangeo is not covered in\nthis tutorial.\n"
  materials:
  - link: topics/climate/tutorials/pangeo-notebook/tutorial.html
    title: Pangeo Notebook in Galaxy - Introduction to Xarray
    type: Tutorial
  tags:
  - climate
  type: Tutorial
  versions:
  - captions:
    - annefou
    date: '2022-03-03'
    galaxy_version: '21.09'
    length: 17M
    link: XFF2yRcYGp0
    speakers:
    - annefou
climate/pangeo/tutorial:
  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.'
  materials:
  - link: topics/climate/tutorials/pangeo/tutorial.html
    title: Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools
    type: Tutorial
  tags:
  - climate
  type: Tutorial
  versions:
  - captions:
    - annefou
    date: '2022-03-03'
    galaxy_version: '21.09'
    length: 1H20M
    link: V43jEJfa6hY
    speakers:
    - annefou
community/welcome:
  description: This short video gives an overview of the worldwide Galaxy community,
    and different ways you can get involved! <strong>Video created by Beatriz Serrano-Solano</strong>.
  materials:
  - external: true
    link: https://galaxyproject.org
    title: galaxyproject.org
    type: GalaxyProject Home
  - external: true
    link: https://galaxyproject.org/use/
    title: Find a Galaxy server near you!
    type: Galaxy servers
  - external: true
    link: https://training.galaxyproject.org
    title: Start learning Galaxy
    type: Galaxy Training Network
  - external: true
    link: https://help.galaxyproject.org/
    title: Galaxy Help Forum
    type: Support
  - external: true
    link: https://www.zotero.org/groups/1732893/galaxy
    title: Zotero
    type: Galaxy Publications
  - external: true
    link: https://galaxyproject.org/community/
    title: Find and Join a community
    type: Galaxy Communities
  - external: true
    link: https://galaxyproject.org/events/
    title: Galaxy Event Horizon
    type: Events
  - external: true
    link: https://galaxyproject.org/mailing-lists/
    title: Stay informed of Galaxy activity!
    type: Mailing Lists
  - external: true
    link: https://galaxyproject.org/community/wg/
    title: Find and join a WG
    type: Galaxy Working Groups
  - external: true
    link: https://github.com/galaxyproject
    title: galaxyproject
    type: GitHub
  - external: true
    link: https://gitter.im/galaxyproject/Lobby
    title: Start talking with the Galaxy Community!
    type: Gitter Chat
  - external: true
    link: https://gitter.im/Galaxy-Training-Network/Lobby
    title: Join the training discussion here!
    type: GTN Gitter
  - external: true
    link: https://galaxyproject.org/events/2021-02-papercuts/
    title: Monthly Collaboration Fest
    type: PaperCuts
  - external: true
    link: https://github.com/galaxyproject/training-material/issues/1712
    title: Everybody Welcome!
    type: GTN CoFest
  - external: true
    link: https://twitter.com/galaxyproject
    title: follow @galaxyproject
    type: GalaxyProject Twitter
  - external: true
    link: https://twitter.com/gxytraining
    title: follow the GTN @gxytraining
    type: GTN Twitter
  tags:
  - community
  title: Meet & Join the Galaxy Community!
  type: Welcome
  versions:
  - captions:
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 5M
    link: -1MPdxmRs8U
    speakers:
    - galaxycommunity
computational-chemistry/htmd-analysis/tutorial:
  description: "Molecular dynamics (MD) is a method to simulate molecular motion by\
    \ iterative application of Newton\u2019s 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)."
  materials:
  - link: topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html
    title: High Throughput Molecular Dynamics and Analysis
    type: Tutorial
  tags:
  - computational-chemistry
  type: Tutorial
  versions:
  - captions:
    - simonbray
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H40M
    link: LjW3nES04bI
    speakers:
    - simonbray
    - chrisbarnettster
contributing/create-new-tutorial-slides/slides:
  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.

    '
  materials:
  - link: topics/contributing/tutorials/create-new-tutorial-slides/slides.html
    title: Creating Slides for the GTN
    type: Slides
  tags:
  - contributing
  type: Lecture
  versions:
  - captions:
    - galaxycommunity
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 5M
    link: Gm1MKAwuLxg
    speakers:
    - awspolly
contributing/create-new-tutorial/tutorial:
  description: This tutorial will go through all of the steps of creating a simple
    tutorial and contributing it to the GTN.
  materials:
  - link: topics/contributing/tutorials/create-new-tutorial/tutorial.html
    title: Creating a new tutorial
    type: Tutorial
  - link: topics/contributing/tutorials/create-new-tutorial-content/tutorial.html
    title: Creating content in Markdown
    type: Related tutorial
  tags:
  - contributing
  type: Tutorial
  versions:
  - captions:
    - EngyNasr
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 42M
    link: Vw9h5kvRH2k
    speakers:
    - bebatut
contributing/gitpod/tutorial:
  description: This tutorial will show you how you can preview your contributions
    to the GTN online using GitPod.
  materials:
  - link: topics/contributing/tutorials/gitpod/tutorial.html
    title: Running the GTN website online using GitPod
    type: Tutorial
  tags:
  - contributing
  type: Tutorial
  versions:
  - captions:
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 20M
    link: _-wnsPttBCo
    speakers:
    - shiltemann
course/welcome-admin:
  description: null
  tags:
  - event
  title: 'Admin Training 2021: Welcome & Course Logistics'
  type: Tutorial
  versions:
  - captions:
    - hexylena
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 9M
    link: 1aWBg1aK-OQ
    speakers:
    - hexylena
course/welcome-gcc2021:
  description: Start here; we will go over all the important things to know to get
    the most out of this workshop
  materials:
  - external: true
    link: https://docs.google.com/presentation/d/11iR7mjnyhl2OX9KDmeE6TrArYeEUwVnnV3cFMFWMBwI/edit?usp=sharing
    type: Slides
  tags:
  - event
  title: 'GCC2021 Training: Welcome & Course Logistics'
  type: Lecture
  versions:
  - captions:
    - shiltemann
    - hexylena
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 15M
    link: 5kjIn1ci4qw
    speakers:
    - hexylena
    - shiltemann
course/welcome-smorg2022:
  description: Start here! We will go over all the important things you need to know
    about this week!
  materials:
  - external: true
    link: https://docs.google.com/presentation/d/e/2PACX-1vQakH_LxLGS5PurJSrmPQH7VY8_UOKpAbUtwsUjpid42QQW5Ds2sH8uD2QQc8rfjH1D0OWpTeSBb8OT/pub?start=false&loop=false&delayms=3000
    type: Slides
  support_channel: general
  tags:
  - event
  title: Start Here! Welcome & Course Logistics
  type: Welcome
  versions:
  - captions:
    - shiltemann
    date: '2022-03-10'
    length: 15M
    link: dU8Cc8z64l0
    speakers:
    - shiltemann
    - hexylena
course/welcome-smorg2023:
  description: Start here! We will go over all the important things you need to know
    about this week!
  materials:
  - external: true
    link: https://docs.google.com/presentation/d/e/2PACX-1vTbVLWzFsiBXaPbGeSdZs2PutWQMHJm2tnttFQPO2ZWujfipZKUDJUCGLMwRMZ5k8o7oST7R_vX2x91/pub?start=false&loop=false&delayms=3000
    type: Slides
  support_channel: general
  tags:
  - event
  title: Start Here! Welcome & Course Logistics
  type: Welcome
  versions:
  - captions:
    - shiltemann
    date: '2023-05-16'
    length: 15M
    link: _Gr-filBzp4
    speakers:
    - shiltemann
    - hexylena
data-science/r-advanced/tutorial:
  description: An advanced tutorial covering downstream analysis of RNA-seq data using
    R.
  materials:
  - link: topics/data-science/tutorials/r-advanced/tutorial.html
    title: Advanced R in Galaxy
    type: Tutorial
  tags:
  - data-science
  type: Tutorial
  versions:
  - captions:
    - ksuderman
    - nagoue
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H
    link: _hWBGdlICqg
    speakers:
    - fpsom
data-science/r-basics/tutorial:
  description: This tutorial will provide an introduction to using R with Rstudio
    in Galaxy.
  materials:
  - link: topics/data-science/tutorials/r-basics/tutorial.html
    title: R basics in Galaxy
    type: Tutorial
  tags:
  - data-science
  type: Tutorial
  versions:
  - captions:
    - s3by01
    - annefou
    - kxk302
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 50M
    link: MKkQDh5Nguc
    speakers:
    - fpsom
data-science/rstudio-galaxy:
  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 <strong>Rstudio Cloud (https://rstudio.cloud/)</strong>
  materials:
  - external: true
    link: https://rstudio.cloud/
    title: Try Rstudio Cloud instead
    type: Rstudio in Galaxy not available?
  tags:
  - galaxy-interface
  title: Running RStudio on Galaxy
  type: Demo
  versions:
  - captions:
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 20M
    link: vN14K74nFZc
    speakers:
    - fpsom
dev/architecture/slides-app-di:
  description: TODO
  materials:
  - link: topics/dev/tutorials/architecture/slides.html
    type: Slides
  - link: topics/dev/tutorials/core-contributing/tutorial.html
    title: Contributing to Galaxy Core
    type: Self-study tutorial
  - external: true
    link: https://bit.ly/gx-arch-vids
    title: Always contains the latest version of these lectures.
    type: Youtube Playlist
  tags:
  - dev
  title: 'Galaxy Code Architecture: app and Dependency Injection'
  type: Lecture
  versions:
  - captions: null
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 15M
    link: Yjl4MIo95nY
    speakers:
    - jmchilton
dev/architecture/slides-ecosystem:
  description: TODO
  materials:
  - link: topics/dev/tutorials/architecture/slides.html
    type: Slides
  - link: topics/dev/tutorials/core-contributing/tutorial.html
    title: Contributing to Galaxy Core
    type: Self-study tutorial
  - external: true
    link: https://bit.ly/gx-arch-vids
    title: Always contains the latest version of these lectures.
    type: Youtube Playlist
  tags:
  - dev
  title: 'Galaxy Code Architecture: Galaxy Ecosystem'
  type: Lecture
  versions:
  - captions: null
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 25M
    link: WbC2NorVKr0
    speakers:
    - jmchilton
dev/architecture/slides-files-directories:
  description: TODO
  materials:
  - link: topics/dev/tutorials/architecture/slides.html
    type: Slides
  - link: topics/dev/tutorials/core-contributing/tutorial.html
    title: Contributing to Galaxy Core
    type: Self-study tutorial
  - external: true
    link: https://bit.ly/gx-arch-vids
    title: Always contains the latest version of these lectures.
    type: Youtube Playlist
  tags:
  - dev
  title: 'Galaxy Code Architecture: Files and Directories'
  type: Lecture Series
  versions:
  - captions: null
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 17M
    link: Nrk0o4EIeUU
    speakers:
    - jmchilton
dev/architecture/slides-models-managers:
  description: TODO
  materials:
  - link: topics/dev/tutorials/architecture/slides.html
    type: Slides
  - link: topics/dev/tutorials/core-contributing/tutorial.html
    title: Contributing to Galaxy Core
    type: Self-study tutorial
  - external: true
    link: https://bit.ly/gx-arch-vids
    title: Always contains the latest version of these lectures.
    type: Youtube Playlist
  tags:
  - dev
  title: 'Galaxy Code Architecture: Models and Managers'
  type: Lecture
  versions:
  - captions: null
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 15M
    link: joiiHN9LlVo
    speakers:
    - jmchilton
dev/architecture/slides-pluggable-components:
  description: TODO
  materials:
  - link: topics/dev/tutorials/architecture/slides.html
    type: Slides
  - link: topics/dev/tutorials/core-contributing/tutorial.html
    title: Contributing to Galaxy Core
    type: Self-study tutorial
  - external: true
    link: https://bit.ly/gx-arch-vids
    title: Always contains the latest version of these lectures.
    type: Youtube Playlist
  tags:
  - dev
  title: 'Galaxy Code Architecture: Pluggable Components'
  type: Lecture
  versions:
  - captions: null
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 45M
    link: wiKv9MDNjA4
    speakers:
    - jmchilton
dev/architecture/slides-principles:
  description: TODO
  materials:
  - link: topics/dev/tutorials/architecture/slides.html
    type: Slides
  - link: topics/dev/tutorials/core-contributing/tutorial.html
    title: Contributing to Galaxy Core
    type: Self-study tutorial
  - external: true
    link: https://bit.ly/gx-arch-vids
    title: Always contains the latest version of these lectures.
    type: Youtube Playlist
  tags:
  - dev
  title: 'Galaxy Code Architecture: Principles'
  type: Lecture
  versions:
  - captions:
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 5M
    link: TKs4IF4ZbeQ
    speakers:
    - jmchilton
dev/architecture/slides-project-management:
  description: TODO
  materials:
  - link: topics/dev/tutorials/architecture/slides.html
    type: Slides
  - link: topics/dev/tutorials/core-contributing/tutorial.html
    title: Contributing to Galaxy Core
    type: Self-study tutorial
  - external: true
    link: https://bit.ly/gx-arch-vids
    title: Always contains the latest version of these lectures.
    type: Youtube Playlist
  tags:
  - dev
  title: 'Galaxy Code Architecture: Project Management'
  type: Lecture
  versions:
  - captions:
    - malloryfreeberg
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 25M
    link: ElOys4F7bzY
    speakers:
    - jmchilton
dev/architecture/slides-web-client:
  description: TODO
  materials:
  - link: topics/dev/tutorials/architecture/slides.html
    type: Slides
  - link: topics/dev/tutorials/core-contributing/tutorial.html
    title: Contributing to Galaxy Core
    type: Self-study tutorial
  - external: true
    link: https://bit.ly/gx-arch-vids
    title: Always contains the latest version of these lectures.
    type: Youtube Playlist
  tags:
  - dev
  title: 'Galaxy Code Architecture: Web Client'
  type: Lecture
  versions:
  - captions: null
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 15M
    link: 9auQWM3tS8I
    speakers:
    - jmchilton
dev/architecture/slides-web-requests:
  description: TODO
  materials:
  - link: topics/dev/tutorials/architecture/slides.html
    type: Slides
  - link: topics/dev/tutorials/core-contributing/tutorial.html
    title: Contributing to Galaxy Core
    type: Self-study tutorial
  - external: true
    link: https://bit.ly/gx-arch-vids
    title: Always contains the latest version of these lectures.
    type: Youtube Playlist
  tags:
  - dev
  title: 'Galaxy Code Architecture: Web Requests'
  type: Lecture
  versions:
  - captions: null
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 35M
    link: vwsxkDMiA10
    speakers:
    - jmchilton
dev/debugging/tutorial/api-test-failure:
  description: What to do when an API test fails.
  materials:
  - link: topics/dev/tutorials/debugging/tutorial.html
    type: Tutorial
  tags:
  - dev
  title: API tests
  type: Tutorial
  versions:
  - captions:
    - jdavcs
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 23M
    link: vYFiFcEuLI0
    speakers:
    - jdavcs
dev/debugging/tutorial/client-linter:
  description: This video covers working through the client linting error hit in the
    previous tutorial.
  materials:
  - link: topics/dev/tutorials/debugging/tutorial.html
    type: Tutorial
  tags:
  - dev
  title: Client Linting
  type: Tutorial
  versions:
  - captions:
    - beatrizserrano
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 6M
    link: YKyP5Y4Y4js
    speakers:
    - assuntad23
dev/debugging/tutorial/client-unit-test:
  description: What to do when your client throws a unit test failure.
  materials:
  - link: topics/dev/tutorials/debugging/tutorial.html
    type: Tutorial
  tags:
  - dev
  title: Client Unit Tests
  type: Tutorial
  versions:
  - captions:
    - beatrizserrano
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 6M
    link: A6LSTCb-rGg
    speakers:
    - assuntad23
dev/debugging/tutorial/intro:
  description: This is the first video in the Debugging Galaxy series.
  materials:
  - link: topics/dev/tutorials/debugging/tutorial.html
    type: Tutorial
  tags:
  - dev
  title: Introduction
  type: Tutorial
  versions:
  - captions:
    - tnabtaf
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 11M
    link: FlFF3TPEfC8
    speakers:
    - assuntad23
    - jdavcs
dev/debugging/tutorial/runtime-error:
  description: How to fix a runtime error
  materials:
  - link: topics/dev/tutorials/debugging/tutorial.html
    type: Tutorial
  tags:
  - dev
  title: Runtime Errors
  type: Tutorial
  versions:
  - captions:
    - jdavcs
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 40M
    link: S7N1WvYGJik
    speakers:
    - jdavcs
dev/debugging/tutorial/selenium:
  description: Selenium is used to test Galaxy development.  Learn more about test
    failure and how to address them.
  materials:
  - link: topics/dev/tutorials/debugging/tutorial.html
    type: Tutorial
  tags:
  - dev
  title: Selenium
  type: Tutorial
  versions:
  - captions:
    - assuntad23
    - jdavcs
    - tnabtaf
    - beatrizserrano
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 18M
    link: 5AAHjxEZb-Y
    speakers:
    - assuntad23
dev/debugging/tutorial/summary:
  description: A summary of wisdom to debug Galaxy with.
  materials:
  - link: topics/dev/tutorials/debugging/tutorial.html
    type: Tutorial
  tags:
  - dev
  title: Debugging Wisdom
  type: Lecture
  versions:
  - captions:
    - tnabtaf
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 3M
    link: _sH1uTKf4ec
    speakers:
    - assuntad23
    - jdavcs
dev/debugging/tutorial/unit-test-failure:
  description: What to do when a unit test fails.
  materials:
  - link: topics/dev/tutorials/debugging/tutorial.html
    type: Tutorial
  tags:
  - dev
  title: Unit Testing
  type: Tutorial
  versions:
  - captions:
    - jdavcs
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 14M
    link: BiANBC78EXM
    speakers:
    - jdavcs
dev/tool-from-scratch/tutorial:
  description: "1. The first step to adding a tool to Galaxy, is to add it to (Bio)Conda.\n\
    \   This tutorial will show you how to do that.\n2. Planemo is the Galaxy tool\
    \ development kit, and will make your tool\n   development process a lot easier!\
    \ This tutorial will show you how to use\n   Planemo to start the tool wrapping\
    \ process, and covers the general\n   structure of a Galaxy tool wrapper.\n3.\
    \ You are now ready to start writing your tool wrapper! This video will\n   show\
    \ you how.\n4. Each tool wrapper also needs a .shed.yml file, which contains some\n\
    \   metadata about the tool.\n5. Here you will learn how to test Galaxy tools\
    \ using Planemo.\n6. Here you will learn how to publish tools in public tool repositories.\n"
  materials:
  - link: topics/dev/tutorials/tool-from-scratch/tutorial.html
    type: Tutorial
  tags:
  - dev
  title: Galaxy Tool Development
  type: Tutorial
  versions:
  - captions:
    - gallardoalba
    date: '2022-03-11'
    galaxy_version: '22.01'
    length: 40M
    link: 33L4B9ir0aQ
    speakers:
    - gallardoalba
  - captions:
    - davebx
    - astrovsky01
    - bernt-matthias
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H40M
    link: videoseries?list=PLNFLKDpdM3B9GhA0FryVV2YX3YL35rENK
    speakers:
    - davebx
    - astrovsky01
    - bernt-matthias
dev/tool-generators-advanced/tutorial:
  description: Hands on demonstration for the Introductory tutorial. Create, run and
    update a "Hello World" tool in Galaxy
  materials:
  - link: topics/dev/tutorials/tool-generators-advanced/tutorial.html
    title: 'ToolFactory: Generating Tools From More Complex Scripts'
    type: Tutorial
  tags:
  - dev
  type: null
  versions:
  - captions:
    - fubar2
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 7M
    link: DK1eKz5TRs4
    speakers:
    - fubar2
dev/tool-generators/tutorial:
  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.

    '
  materials:
  - link: topics/dev/tutorials/tool-generators/tutorial.html
    type: Tutorial
  tags:
  - dev
  type: null
  versions:
  - captions:
    - fubar2
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 30M
    link: 8nKBfVM6240
    speakers:
    - fubar2
ecology/Obitools-metabarcoding/tutorial:
  description: 'Based on this OBITools official tutorial, you will learn here how
    to

    analyze DNA metabarcoding data produced on Illumina sequencers

    '
  materials:
  - link: topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html
    type: Tutorial
  tags:
  - ecology
  type: Lecture
  versions:
  - captions:
    - yvanlebras
    date: '2022-03-03'
    galaxy_version: '21.09'
    length: 1H15M
    link: o2cUvb_lmLs
    speakers:
    - yvanlebras
ecology/PAMPA-toolsuite-tutorial/tutorial:
  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.

    '
  materials:
  - link: topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html
    type: Tutorial
  tags:
  - ecology
  type: Lecture
  versions:
  - captions:
    - colineroyaux
    date: '2022-03-03'
    galaxy_version: '21.09'
    length: 2H
    link: leMPC2Ckehc
    speakers:
    - colineroyaux
ecology/biodiversity-data-exploration/tutorial:
  description: ''
  materials:
  - link: topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html
    type: Tutorial
  tags:
  - ecology
  type: Lecture
  versions:
  - captions:
    - onorvez
    date: '2022-03-03'
    galaxy_version: '21.09'
    length: 1H
    link: rWfPr-5F3GQ
    speakers:
    - onorvez
epigenetics/atac-seq/slides:
  description: This lecture will introduce the basic concepts involved in ATAC-Seq
    analysis.
  materials:
  - link: topics/epigenetics/tutorials/atac-seq/slides.html
    type: Slides
  tags:
  - epigenetics
  type: Lecture
  versions:
  - captions:
    - lldelisle
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 15M
    link: 2jPNNd5YJNM
    speakers:
    - lldelisle
epigenetics/atac-seq/tutorial:
  description: This tutorial will walk you through a ATAC-Seq data analysis.
  materials:
  - link: topics/epigenetics/tutorials/atac-seq/tutorial.html
    title: ATAC-Seq data analysis
    type: Tutorial
  tags:
  - epigenetics
  type: Tutorial
  versions:
  - captions:
    - hrhotz
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H50M
    link: Zc-bl6ZfcX4
    speakers:
    - heylf
galaxy-interface/collections/tutorial:
  description: null
  materials:
  - link: topics/galaxy-interface/tutorials/collections/tutorial.html
    title: Using dataset collections
    type: Tutorial
  tags:
  - galaxy-interface
  type: Tutorial
  versions:
  - link: uN6nP3I7QLE
    captions:
    date: '2023-05-09'
    length: 13M
    speakers:
    - delphine-l
  - captions:
    - annefou
    - mariipia10
    date: '2021-08-09'
    length: 11M
    link: uZUt9XIHUQo
    speakers:
    - nekrut
galaxy-interface/interactive-tools:
  description: This demo videos shows you how you can run Interactive tools such as
    RStudio and Jupyter notebooks within Galaxy.
  tags:
  - galaxy-intro
  - galaxy
  title: Interactive Tools
  type: Demo
  versions:
  - captions:
    - shiltemann
    date: '2022-07-07'
    length: 15M
    link: 21Eo3QlKuoA
    speakers:
    - hexylena
galaxy-interface/ncbi-sarf/slides:
  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.
  materials:
  - link: topics/galaxy-interface/tutorials/ncbi-sarf/slides.html
    title: Introduction to SRA Aligned Read Format and Cloud Metadata for SARS-CoV-2
    type: Slides
  tags:
  - galaxy-interface
  type: Lecture
  versions:
  - captions:
    - prodromus
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 15M
    link: siLP71B9gm4
    speakers:
    - prodromus
galaxy-interface/ncbi-sarf/tutorial:
  description: This tutorial will walk you through accessing and using SRA Aligned
    read format in Galaxy.
  materials:
  - link: topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.html
    title: SRA Aligned Read Formats to Speed Up SARS-CoV-2 data Analysis
    type: Tutorial
  - link: topics/variant-analysis/tutorials/sars-cov-2/tutorial.html
    title: 'From NCBI''s Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant
      analysis'
    type: Related Tutorial
  tags:
  - galaxy-interface
  type: Tutorial
  versions:
  - captions:
    - prodromus
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 40M
    link: ogu-NBTP-DM
    speakers:
    - prodromus
galaxy-interface/upload-rules:
  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..
  materials:
  - link: topics/galaxy-interface/tutorials/upload-rules/tutorial.html
    type: Tutorial
  - link: topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.html
    type: Tutorial
  tags:
  - galaxy-interface
  type: Tutorial
  versions:
  - captions:
    - assuntad23
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 22M
    link: 1MWHVRWXpyA
    speakers:
    - assuntad23
galaxy-interface/upload-to-ena:
  description: "So you\u2019ve used Galaxy workflows to analyze your SARS-CoV-2 samples?\
    \ Learn in this tutorial how to export results to your favorite datastore."
  materials: []
  tags:
  - sars-cov2
  - galaxy-interface
  title: Uploading data to ENA
  type: Lecture & Tutorial
  versions:
  - captions:
    - hexylena
    date: '2021-08-09'
    length: 10M
    link: -5U0sINjoig
    speakers:
    - wm75
galaxy-interface/workflow-automation:
  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.
  materials:
  - external: true
    link: https://docs.microsoft.com/en-us/windows/wsl/install-win10
    title: Installing WSL on Windows
    type: Get Set Up (Windows)
  - link: topics/galaxy-interface/tutorials/workflow-automation/tutorial.html
    type: Tutorial
  tags:
  - galaxy-interface
  type: Tutorial
  versions:
  - captions:
    - simonbray
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 30M
    link: o39QjVnLG68
    speakers:
    - simonbray
galaxy-interface/workflow-parameters/tutorial:
  description: To make a workflow reusable with slightly different settings you can
    define and use workflow parameters.
  materials:
  - link: topics/galaxy-interface/tutorials/workflow-parameters/tutorial.html
    title: Workflow Parameters
    type: Tutorial
  tags:
  - galaxy-interface
  type: Tutorial
  versions:
  - captions:
    - mvdbeek
    date: '2022-07-06'
    length: 30M
    link: otvEuDlCye0
    speakers:
    - mvdbeek
galaxy-interface/workflow-reports/tutorial:
  description: Learn how to view, customize and share Galaxy workflow reports
  materials:
  - link: topics/galaxy-interface/tutorials/workflow-reports/tutorial.html
    title: Workflow Reports
    type: Tutorial
  tags:
  - galaxy-interface
  type: Tutorial
  versions:
  - captions:
    - shiltemann
    date: '2022-07-06'
    length: 30M
    link: hrZhpsiGaPM
    speakers:
    - shiltemann
galaxy/intro:
  description: This video will introduce the Galaxy data analysis platform, and give
    a short demo on how to use it.
  materials:
  - link: topics/introduction/tutorials/galaxy-intro-short/slides.html
    title: A Short Introduction to Galaxy
    type: Related Slides
  tags:
  - galaxy-intro
  - galaxy
  title: A Very Short Introduction to Galaxy
  type: Lecture & Demo
  versions:
  - captions:
    - nekrut
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 10M
    link: VZoz3k5EehI
    speakers:
    - nekrut
galaxy/intro2:
  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.
  materials:
  - external: true
    link: https://docs.google.com/presentation/d/1rOGp4o_Dc-QIHS4YT4HizdfXTVhJB1HwPPZkSDuMhig/edit#slide=id.gbc9627d000_0_346
    title: Overview Presentation
    type: Slides
  - link: topics/introduction/tutorials/galaxy-intro-strands/tutorial.html
    title: Introduction to Genomics and Galaxy
    type: Tutorial
  - link: topics/galaxy-interface/tutorials/history-to-workflow/tutorial.html
    title: Extracting Workflows from Histories
    type: Tutorial
  tags:
  - galaxy-intro
  - galaxy
  title: Your First Galaxy Analysis
  type: Tutorial
  versions:
  - captions:
    - tnabtaf
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H30M
    link: 1UPCrQxGwcU
    speakers:
    - tnabtaf
genome-annotation/annotation-with-prokka/slides:
  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.
  materials:
  - link: topics/genome-annotation/tutorials/annotation-with-prokka/slides.html
    type: Slides
  tags:
  - genome-annotation
  type: Lecture
  versions:
  - captions:
    - abretaud
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 3M
    link: eqHy-Cc7k4Q
    speakers:
    - awspolly
genome-annotation/annotation-with-prokka/tutorial:
  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."
  materials:
  - link: topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html
    type: Tutorial
  tags:
  - genome-annotation
  type: Tutorial
  versions:
  - captions:
    - abretaud
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 20M
    link: B8pIQZPf21Y
    speakers:
    - abretaud
genome-annotation/apollo/slides:
  description: This lecture gives a quick overview of Apollo
  materials:
  - link: topics/genome-annotation/tutorials/apollo/slides.html
    type: Slides
  tags:
  - genome-annotation
  type: Lecture
  versions:
  - captions:
    - abretaud
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 5M
    link: ailUycRVHtE
    speakers:
    - awspolly
genome-annotation/apollo/tutorial:
  description: In this tutorial you will get some hands-on experience using Apollo
    in Galaxy
  materials:
  - link: topics/genome-annotation/tutorials/apollo/tutorial.html
    type: Tutorial
  - external: true
    link: https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html
    type: Apollo User's Guide
  tags:
  - genome-annotation
  type: Tutorial
  versions:
  - captions:
    - abretaud
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H
    link: ywK1fhM-QFU
    speakers:
    - abretaud
genome-annotation/crispr-screen/slides:
  description: This lecture will introduce the basic concepts involved in CRISPR screen
    analysis.
  materials:
  - link: topics/genome-annotation/tutorials/crispr-screen/slides.html
    type: Slides
  tags:
  - crispr
  type: Lecture
  versions:
  - captions:
    - mblue9
    date: '2022-03-10'
    galaxy_version: '21.09'
    length: 3M
    link: MNT9gB5_RMg
    speakers:
    - awspolly
genome-annotation/crispr-screen/tutorial:
  description: This tutorial will walk you through a CRISPR screen analysis.
  materials:
  - link: topics/genome-annotation/tutorials/crispr-screen/tutorial.html
    title: CRISPR screen analysis
    type: Tutorial
  tags:
  - crispr
  type: Tutorial
  versions:
  - captions:
    - mblue9
    date: '2022-03-10'
    galaxy_version: '21.09'
    length: 45M
    link: wavAf_2ytWg
    speakers:
    - mblue9
genome-annotation/funannotate/tutorial:
  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).

    '
  materials:
  - link: topics/genome-annotation/tutorials/funannotate/tutorial.html
    type: Tutorial
  tags:
  - genome-annotation
  type: Tutorial
  versions:
  - link: p0NBxZk5964
    speakers:
    - abretaud
    date: '2023-05-12'
    galaxy_version: '23.01'
    length: 1H10M
    captions: [abretaud]
  - captions:
    - abretaud
    date: '2022-03-03'
    galaxy_version: '21.09'
    length: 1H10M
    link: r-wU6BhqIpk
    speakers:
    - abretaud
genome-annotation/repeatmasker/tutorial:
  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.
  materials:
  - link: topics/genome-annotation/tutorials/repeatmasker/tutorial.html
    type: Tutorial
  tags:
  - genome-annotation
  type: Tutorial
  versions:
  - link: 7tYEDmAvHD4
    speakers:
    - abretaud
    length: 18M
    captions:
    - abretaud
    galaxy_version: '23.01'
    date: '2023-05-10'
  - captions:
    - abretaud
    date: '2022-03-03'
    galaxy_version: '21.09'
    length: 16M
    link: AYAvjwm4cnM
    speakers:
    - abretaud
genome-annotation/tnseq-lecture:
  description: 'This lecture talks about the basics of TnSeq analysis

    '
  materials:
  - external: true
    link: https://www.dropbox.com/sh/ayix345v11n69es/AABJerasUhiD4JfSgS3g0kS7a?dl=0&preview=TnSeq-GTapas-2022.pdf
    type: Non-GTN Lecture
  tags:
  - genome-annotation
  title: Essential genes detection with Transposon insertion sequencing (Lecture)
  type: Lecture
  versions:
  - captions: null
    date: '2022-03-10'
    galaxy_version: '21.09'
    length: 10M
    link: ehqObidPhcE
    speakers:
    - delphine-l
introduction/galaxy-intro-101-everyone/tutorial:
  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.
  materials:
  - link: topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html
    title: Galaxy 101 for Everyone
    type: Tutorial
  tags:
  - galaxy
  type: Tutorial
  versions:

  - captions:
    date: '2023-05-01'
    length: 20M
    galaxy_version: '23.0'
    link: 64oS5uXVRV0
    speakers:
      - astrovsky01

  - captions:
    - tnabtaf
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H15M
    link: dguN6Xw2Azs
    speakers:
    - annefou
    - rwinand

introduction/galaxy-intro-101/tutorial:
  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
  materials:
  - link: topics/introduction/tutorials/galaxy-intro-101/tutorial.html
    type: Tutorial
  - external: true
    link: https://usegalaxy.eu/u/wolfgang-maier/h/galaxy-101
    type: History on GalaxyEU
  tags:
  - introduction
  type: Tutorial
  versions:
  - captions:
    - shiltemann
    date: '2021-07-21'
    length: 13M
    link: D5HgJWdfOWw
    speakers:
    - nekrut
introduction/galaxy-intro-ngs-data-managment:
  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).
  materials:
  - link: topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html
    title: NGS data logistics
    type: Tutorial
  tags:
  - introduction
  type: Demo
  versions:
  - captions:
    - nekrut
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 15M
    link: 9mIL0tIfZ_o
    speakers:
    - nekrut
variant-analysis/sars-cov-2:
  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.
  materials:
  - link: topics/variant-analysis/tutorials/sars-cov-2/tutorial.html
    title: 'From NCBI''s Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis'
    type: Tutorial
  tags:
  - variant-analysis
  type: Demo
  versions:
  - captions:
    - nekrut
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 15M
    link: 9mIL0tIfZ_o
    speakers:
    - nekrut
metagenomics/clinical-applications:
  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.
  materials: []
  tags:
  - metagenomics
  title: Nanopore Whole Bacterial Genome Sequencing in a Clinical Setting
  type: Lecture
  versions:
  - captions:
    - hexylena
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 30M
    link: icXMqMut6PY
    speakers:
    - aheikema
metagenomics/introduction/slides:
  description: This lecture briefly introduces 16S sequencing, a popular technique
    used for taxonomic profiling of microbial communities.
  materials:
  - link: topics/metagenomics/slides/introduction.html
    title: Introduction to Metagenomics Analyses
    type: Slides
  tags:
  - metagenomics
  type: Lecture
  versions:
  - captions:
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 15M
    link: 9OY1mklWuK0
    speakers:
    - shiltemann
metagenomics/metatranscriptomics:
  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.
  materials:
  - external: true
    link: https://drive.google.com/file/d/11TOrL7Kxgel71AT1rBc4DqjaUh3QB2G_/view?usp=sharing
    type: Slides from video
  - link: topics/metagenomics/tutorials/metatranscriptomics/slides.html
    title: Introduction to Metatranscriptomics
    type: Related Slides
  - link: topics/metagenomics/tutorials/metatranscriptomics/tutorial.html
    type: Tutorial
  tags:
  - metagenomics
  type: Tutorial
  versions:
  - link: HNYop3vLpoM
    date: '2023-05-17'
    speakers:
    - paulzierep
    captions: []
    length: 1H5M
    galaxy_version: "23.01"
  - captions:
    - EngyNasr
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H30M
    link: EMaos5u1_a8
    speakers:
    - pratikdjagtap
    - timothygriffin
    - subinamehta
    - shiltemann
metagenomics/mothur-miseq-sop-short/tutorial:
  description: This lecture briefly introduces 16S sequencing, a popular technique
    used for taxonomic profiling of microbial communities.
  materials:
  - link: topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html
    type: Tutorial
  tags:
  - metagenomics
  type: Tutorial
  versions:
  - captions:
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H40M
    link: mto4Nl-q7Kk
    speakers:
    - shiltemann
metagenomics/plasmid-metagenomics-nanopore/tutorial:
  description: This tutorial will guide you through the process of assembling your
    Nanopore-sequenced bacterial samples and determining the presence of antibiotic
    resistance genes.
  materials:
  - link: topics/metagenomics/tutorials/plasmid-metagenomics-nanopore/tutorial.html
    title: Antibiotic resistance detection of plasmid data
    type: Tutorial
  - link: topics/metagenomics/tutorials/nanopore-16S-metagenomics/tutorial.html
    title: 16S Microbial analysis with Nanopore data
    type: Related Tutorial
  tags:
  - metagenomics
  type: Tutorial
  versions:
  - captions:
    - bebatut
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 45M
    link: ECIl8ZU1Wko
    speakers:
    - willemdek11

metagenomics/pathogen-detection-from-nanopore-foodborne-data/tutorial:
  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

  materials:
  - link: topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.thml
    type: Tutorial
  tags:
   - metagenomics
  versions:
  - link: gQHb_jkj-Z0
    date: '2023-05-01'
    galaxy_version: '23.01'
    length: 1H45M
    speakers:
    - EngyNasr
    captions:
    - EngyNasr

metagenomics/beer-data-analysis/tutorial:
  description:
  tags:
  - metagenomics
  type: Tutorial
  materials:
  - link: topics/metagenomics/tutorials/beer-data-analysis/tutorial.html
    type: Tutorial
  versions:
  - link: PJeS06yiJUM
    speakers:
    - bebatut
    captions: [sophia120199]
    date: '2023-05-10'
    galaxy_version: '23.01'
    length: 1H5M

metagenomics/metagenomics-assembly/tutorial:
  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.
  tags:
  - metagenomics
  - assembly
  materials:
  - link: topics/metagenomics/tutorials/metagenomics-assembly/tutorial.html
    type: tutorial
  versions:
  - link: 1ZYGy85Im7w
    date: '2023-05-02'
    speakers:
    - bebatut
    galaxy_version: '23.01'
    length: 1H
    captions:
    - bebatut
    - sophia120199


proteogenomics/introduction/slides:
  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.
  materials:
  - external: true
    link: https://drive.google.com/file/d/1rqzf6Mrk9cMuQ2531tM6RpltPLrDCrgh/view?usp=sharing
    type: Slides
  tags:
  - proteogenomics
  title: Introduction to Proteogenomics
  type: Lecture
  versions:
  - captions:
    - emmaleith
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 20M
    link: WpH101OPrG0
    speakers:
    - timothygriffin
proteomics/encyclopedia/slides:
  description: This lecture will introduce EncyclopeDIA.
  materials:
  - link: topics/proteomics/tutorials/encyclopedia/tutorial.html
    type: Tutorial
  tags:
  - proteomics
  type: Lecture
  versions:
  - captions:
    - emmaleith
    date: '2021-06-25'
    galaxy_version: '21.01'
    length: 20M
    link: EGWTFWeI5gg
    speakers:
    - jj-umn
    - pratikdjagtap
proteomics/encyclopedia/tutorial:
  description: This tutorial will walk you through an analysis with EncyclopeDIA step
    by step.
  materials:
  - link: topics/proteomics/tutorials/encyclopedia/tutorial.html
    type: Tutorial
  tags:
  - proteomics
  type: Tutorial
  versions:
  - captions:
    - mtekman
    date: '2021-06-25'
    galaxy_version: '21.01'
    length: 30M
    link: eCEjHtbZLVg
    speakers:
    - emmaleith
proteomics/introduction/slides:
  description: "This lecture will provide an introduction to mass spectrometry (MS)\
    \ based proteomics analysis. <strong>Slides created by Melanie F\xF6ll</strong>."
  materials:
  - link: topics/proteomics/slides/introduction.html
    title: Introduction to proteomics, protein identification, quantification and
      statistical modelling
    type: Slides
  tags:
  - proteomics
  type: Lecture
  versions:
  - captions:
    - foellmelanie
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 20M
    link: 2C96AvrFT38
    speakers:
    - awspolly
proteomics/maxquant-msstats-dda-lfq/tutorial:
  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\u2019ll use two popular quantitative\
    \ proteomics software: MaxQuant and MSstats."
  materials:
  - link: topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html
    title: MaxQuant and MSstats for the analysis of label-free data
    type: Tutorial
  - external: true
    link: https://usegalaxy.eu/u/melanie-foell/h/maxquant-and-msstats-label-free-proteomics-training
    title: Galaxy History of this tutorial
    type: Example History
  tags:
  - proteomics
  type: Tutorial
  versions:
  - captions:
    - foellmelanie
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H
    link: IXdLAt2PAT4
    speakers:
    - foellmelanie
proteomics/metaproteomics/tutorial:
  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.
  materials:
  - link: topics/proteomics/tutorials/metaproteomics/tutorial.html
    type: Tutorial
  tags:
  - proteomics
  type: Demo
  versions:
  - captions:
    - emmaleith
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H
    link: 3_yaPp-RCFw
    speakers:
    - pratikdjagtap
proteomics/pandemic/external:
  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\
    \ \u2013 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)](https://doi.org/10.1186/s12014-021-09321-1))\
    \ and co-infecting pathogen peptides ([10.1021/acs.jproteome.0c00822](https://doi.org/10.1021/acs.jproteome.0c00822))."
  materials:
  - external: true
    link: https://drive.google.com/file/d/1anBPmGRWEVp9pBLZ_JInWV7iWrBpyCDs/view?usp=sharing
    type: Slides
  - external: true
    link: https://usegalaxy.eu/workflow/export_to_file?id=8a85663218676b59
    type: Workflow
  tags:
  - proteomics
  title: Pandemics Research using Mass Spectrometry
  type: Lecture & Demo
  versions:
  - captions:
    - emmaleith
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 35M
    link: CI35gTmZoqM
    speakers:
    - timothygriffin
    - subinamehta
    - andrewr
    - pratikdjagtap
proteomics/proteogenomics-dbcreation/tutorial:
  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.
  materials:
  - link: topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html
    type: Tutorial
  tags:
  - proteomics
  type: Tutorial
  versions:
  - captions:
    - emmaleith
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 40M
    link: b_kZf8mXHdo
    speakers:
    - jj-umn
proteomics/proteogenomics-dbsearch/tutorial:
  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.
    <strong> If you would like to view the results yourself, we provide example histories
    in the FAQ document</strong>
  materials:
  - link: topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html
    type: Tutorial
  - external: true
    link: https://docs.google.com/presentation/d/1gAOJ7WQI1CEc3VeSm_fcvjg_GTxTCZ1N/edit#slide=id.p2
    type: Slides
  tags:
  - proteomics
  type: Demo
  versions:
  - captions:
    - emmaleith
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 30M
    link: q1OjmTcbvBA
    speakers:
    - andrewr
proteomics/proteogenomics-novel-peptide-analysis/tutorial:
  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). <strong> If you would
    like to view the results yourself, we provide example histories in the FAQ document</strong>
  materials:
  - link: topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html
    type: Tutorial
  tags:
  - proteomics
  type: Demo
  versions:
  - captions:
    - subinamehta
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 40M
    link: Ku274KwFh1Y
    speakers:
    - subinamehta
proteomics/proteome_annotation/tutorial:
  description: This tutorial covers an annotation pipeline for a protein list identified
    by LC-MS/MS experiments.
  materials:
  - link: topics/proteomics/tutorials/proteome_annotation/tutorial.html
    title: Annotating a protein list identified by LC-MS/MS experiments
    type: Tutorial
  tags:
  - proteomics
  type: Tutorial
  versions:
  - captions:
    - combesf
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 30M
    link: qG7GZc6BeGY
    speakers:
    - yvesvdb
sars-cov2/observablehq:
  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.

    '
  materials: []
  tags:
  - sars-cov2
  title: Using and Customising ObservableHQ
  type: Demo
  versions:
  - captions:
    - assuntad23
    date: '2021-12-08'
    galaxy_version: '21.01'
    length: 15M
    link: owZ8AToX4sE
    speakers:
    - sergeipond
sars-cov2/upload-ena:
  description: ''
  materials: []
  tags:
  - sars-cov2
  title: Upload to ENA
  type: Demo
  versions:
  - captions:
    - mariipia10
    - assuntad23
    date: '2021-12-08'
    galaxy_version: '21.01'
    length: 10M
    link: sEjhWAtmAn4
    speakers:
    - miguelroncoroni
sars-cov2/usegalaxy-star-bot:
  description: "See in this demo how, on usegalaxy.*, we\u2019ve 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."
  materials: []
  tags:
  - sars-cov2
  title: The usegalaxy.* SARS-CoV-2 Bot in Action
  type: Demo
  versions:
  - captions:
    - hexylena
    date: '2021-08-09'
    length: 40M
    link: IRxja8bZ-MU
    speakers:
    - wm75
sars-cov2/using-galaxy:
  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'
  materials: []
  tags:
  - sars-cov2
  title: SARS-CoV-2 Monitoring and Analysis with Galaxy
  type: Tutorial
  versions:
  - captions:
    - mariipia10
    date: '2021-08-09'
    length: 13M
    link: luxFraFJTc4
    speakers:
    - wm75
sars-cov2/viral-beacon/slides:
  description: "How to visualize tens of thousands of SARS-CoV-2 analysis results?\
    \ Learn about the Viral Beacon project\u2019s solution!\n"
  materials:
  - external: true
    link: https://drive.google.com/file/d/1yCHOi1EGKpkH-3XpKTKNKpFjwYAWKSVx/preview
  tags:
  - sars-cov2
  title: Introduction to viral Beacon
  type: Demo
  versions:
  - captions:
    - assuntad23
    date: '2021-12-08'
    galaxy_version: '21.01'
    length: 24M
    link: R_4yUMPk7eY
    speakers:
    - babitasingh


virology/sequencing-spectrum-viral-genomes:
  title: Sequencing data analysis for a spectrum of viral genomes
  description:
  type: Lecture
  tags:
  - variant-analysis
  - virology
  versions:
  - link: CAwldVPimkY
    speakers:
    - wm75
    date: '2023-05-04'
    length: 12M
    captions:



sequence-analysis/human-reads-removal/tutorial:
  description: null
  materials:
  - link: topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html
    title: Removal of human reads from SARS-CoV-2 sequencing data
    type: Tutorial
  - external: true
    link: https://usegalaxy.eu/u/wolfgang-maier/h/removal-of-human-reads-from-sars-cov-2-sequencing-data
    title: Example History
    type: Example History
  tags:
  - sequence-analysis
  type: Tutorial
sequence-analysis/mapping/slides:
  description: This lecture covers the basic concepts involved in mapping sequencing
    reads to a reference genome.
  materials:
  - link: topics/sequence-analysis/tutorials/mapping/slides.html
    title: Mapping
    type: Slides
  tags:
  - sequence-analysis
  type: Lecture
  versions:
  - captions:
    - blankenberg
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 10M
    link: 7FhHb8EV3EU
    speakers:
    - pvanheus
sequence-analysis/mapping/tutorial:
  description: In this tutorial you will map sequencing data to a reference genome,
    and explore the mapped reads in a genome browser.
  materials:
  - link: topics/sequence-analysis/tutorials/mapping/tutorial.html
    title: Mapping
    type: Tutorial
  tags:
  - sequence-analysis
  type: Tutorial
  versions:
  - captions:
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 20M
    link: 1wm-62E2NkY
    speakers:
    - pvanheus
sequence-analysis/quality-control/slides:
  description: This lecture goes over the concepts involved in assessing the quality
    of your sequencing data.
  materials:
  - link: topics/sequence-analysis/tutorials/quality-control/slides.html
    title: Introduction to Quality Control
    type: Slides
  tags:
  - sequence-analysis
  type: Lecture
  versions:
  - captions:
    - ennovytje
    - nagoue
    - hexylena
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 40M
    link: BWonTPS4zB8
    speakers:
    - heylf
sequence-analysis/quality-control/tutorial:
  description: In this tutorial you will get some hand-on experience performing a
    quality assessment on sequencing data.
  materials:
  - link: topics/sequence-analysis/tutorials/quality-control/tutorial.html
    type: Tutorial
  tags:
  - sequence-analysis
  type: Tutorial
  versions:
  - captions:
    - bebatut
    - nagoue
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H10M
    link: QJRlX2hWDKM
    speakers:
    - heylf
statistics/CNN:
  description: This hands-on tutorial covers Convolutional Neural Networks (CNN)
  materials:
  - link: topics/statistics/tutorials/CNN/slides.html
    title: Convolutional Neural Networks
    type: Slides
  - link: topics/statistics/tutorials/CNN/tutorial.html
    title: Convolutional Neural Networks
    type: Tutorial
  tags:
  - statistics
  title: Convolutional Neural Networks (CNN)
  type: Tutorial
  versions:
  - captions:
    - FilipposZ
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H
    link: P1NVYOJrv_4
    speakers:
    - kxk302
statistics/FNN:
  description: This hands-on tutorial covers Feedforward Neural Networks (FNN)
  materials:
  - link: topics/statistics/tutorials/FNN/slides.html
    title: Feedforward Neural Networks
    type: Slides
  - link: topics/statistics/tutorials/FNN/tutorial.html
    title: Feedforward Neural Networks
    type: Tutorial
  tags:
  - statistics
  title: Feedforward Neural Networks (FNN)
  type: Tutorial
  versions:
  - captions:
    - kxk302
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H10M
    link: VbzJDkyPL4A
    speakers:
    - kxk302
statistics/RNN:
  description: This hands-on tutorial covers Recurrenct Neural Networks (RNN)
  materials:
  - link: topics/statistics/tutorials/RNN/slides.html
    title: Recurrent Neural Networks
    type: Slides
  - link: topics/statistics/tutorials/RNN/tutorial.html
    title: Recurrent Neural Networks
    type: Tutorial
  tags:
  - statistics
  title: Recurrent Neural Networks (RNN)
  type: Tutorial
  versions:
  - captions:
    - kxk302
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 50M
    link: 1dwzEhjOAmw
    speakers:
    - kxk302
statistics/classification_machinelearning/tutorial:
  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.
  materials:
  - link: topics/statistics/tutorials/classification_machinelearning/tutorial.html
    type: Tutorial
  - external: true
    link: https://docs.google.com/presentation/d/1lAYCZ-g6y8cC1aH68FWL6gkRRI2srXSHuJwaaYAQZaU/edit?usp=sharing
    title: Classification in Machine Learning
    type: Slides
  support_channel: machine_learning_classification
  tags:
  - statistics
  type: Tutorial
  versions:
  - captions:
    - anuprulez
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H50M
    link: Gz2OdRPS2Nk
    speakers:
    - anuprulez
statistics/fruit_360:
  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-Bold\xFA\
    \ 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\u2019\
    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 (Mure\u015Fan and Oltean\
    \ 2018)\n"
  materials:
  - link: topics/statistics/tutorials/fruit_360/slides.html
    type: Slides
  - link: topics/statistics/tutorials/fruit_360/tutorial.html
    type: Tutorial
  tags:
  - statistics
  type: Tutorial
  versions:
  - captions:
    - kxk302
    date: '2022-01-19'
    galaxy_version: '21.09'
    length: 1H
    link: EX8gZ1lxhNY
    speakers:
    - kxk302
statistics/intro-to-ml-with-r/tutorial:
  description: "This is an Introduction to Machine Learning in R, in which you\u2019\
    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\u2019ll 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."
  materials:
  - link: topics/statistics/tutorials/intro-to-ml-with-r/tutorial.html
    title: Introduction to Machine Learning using R
    type: Tutorial
  tags:
  - statistics
  type: Tutorial
  versions:
  - captions:
    - MariaTsayo
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H30M
    link: RT-g6KyAGdE
    speakers:
    - fpsom
statistics/machine-learning/intro:
  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.
  materials:
  - external: true
    link: https://docs.google.com/presentation/d/1RZtXFk8qz6wmPsIKnMte3Y4SvmI_nD2vIyeSEvYR6RA/edit?usp=sharing
    title: Introduction to Machine Learning
    type: Slides
  support_channel: machine_learning_introduction
  tags:
  - statistics
  title: Introduction to Machine Learning
  type: Lecture
  versions:
  - captions:
    - anuprulez
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 15M
    link: ix58oj8n8nA
    speakers:
    - anuprulez
statistics/regression_machinelearning/tutorial:
  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.
  materials:
  - link: topics/statistics/tutorials/regression_machinelearning/tutorial.html
    type: Tutorial
  - external: true
    link: https://docs.google.com/presentation/d/16Ct2wJmLz4YI2rF9Y1SxcFWfSdVyJVoBy3YynBRDB0Q/edit?usp=sharing
    title: Regression in Machine Learning
    type: Slides
  tags:
  - statistics
  type: Lecture & Tutorial
  versions:
  - captions:
    - anuprulez
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 1H29M
    link: qxaWQjtEOzM
    speakers:
    - anuprulez
synthetic-biology/basic_assembly_analysis/demo:
  materials:
  - link: topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.html
    type: Tutorial
  tags:
  - synthetic-biology
  title: Designing plasmids encoding predicted pathways by using the BASIC assembly
    method
  type: Demo
  versions:
  - captions:
    - kenza12
    date: '2022-05-11'
    length: 3M
    link: 0ItpHuSM7t0
    speakers:
    - breakthewall
synthetic-biology/pathway_analysis/demo:
  materials:
  - link: topics/synthetic-biology/tutorials/pathway_analysis/tutorial.html
    type: Tutorial
  tags:
  - synthetic-biology
  title: Evaluating and ranking a set of pathways based on multiple metrics
  type: Demo
  versions:
  - captions:
    - kenza12
    date: '2022-09-26'
    length: 5M
    link: 240oxe8unnU
    speakers:
    - breakthewall
synthetic-biology/retrosynthesis_analysis/demo:
  materials:
  - link: topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.html
    type: Tutorial
  tags:
  - synthetic-biology
  title: Generating theoretical possible pathways for the production of Lycopene in
    E.Coli using Retrosynthesis tools.
  type: Demo
  versions:
  - captions:
    - kenza12
    date: '2022-06-23'
    length: 5M
    link: nnE3Ip94D8I
    speakers:
    - breakthewall
single-cell/bulk-music/tutorial:
  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.

    '
  materials:
  - link: topics/single-cell/tutorials/bulk-music/tutorial.html
    type: Tutorial
  tags:
  - transcriptomics
  - single-cell
  type: Tutorial
  versions:
  - captions:
    - mtekman
    - nomadscientist
    date: '2021-03-08'
    galaxy_version: '21.09'
    length: 20M
    link: nfAUXP3W-jM
    speakers:
    - nomadscientist

transcriptomics/de-novo/tutorial:
  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.
  materials:
  - link: topics/transcriptomics/tutorials/de-novo/tutorial.html
    type: Tutorial
  - external: true
    link: https://europepmc.org/article/MED/25319994
    title: Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive
      large-scale reprogramming of gene expression during hematopoiesis.
    type: Publication
  - external: true
    link: https://zenodo.org/record/583140#.YMpdBTZKjt1
    title: Zenodo
    type: Training data
  tags:
  - transcriptomics
  type: Tutorial
  versions:
  - captions:
    - malloryfreeberg
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 48M
    link: WrOIpCxba78
    speakers:
    - malloryfreeberg
single-cell/scrna-case_monocle3-trajectories:
  description:
  materials:
    - link: topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html
      type: Tutorial
  tags:
    - single-cell
    - transcriptomics
  type: Tutorial
  versions:
    - link: Espl6qSbu3Y
      date: '2023-04-11'
      length: 15M
      speakers:
        - wee-snufkin
      captions:
        - wee-snufkin
single-cell/scrna-case_alevin/tutorial:
  description: "This tutorial will take you from raw FASTQ files to a cell x gene\
    \ data matrix in AnnData format. What\u2019s a data matrix, and what\u2019s AnnData\
    \ format? Well you\u2019ll find out! Importantly, this is the first step in processing\
    \ single cell data in order to start analysing it."
  materials:
  - link: topics/single-cell/tutorials/scrna-case_alevin/tutorial.html
    type: Tutorial
  tags:
  - single-cell
  - transcriptomics
  type: Demo
  versions:
  - captions:
    - nomadscientist
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 30M
    link: 3ytm2AU6QUc
    speakers:
    - nomadscientist

single-cell/scrna-case_alevin-combine-datasets/tutorial:
  description: ''
  materials:
  - link: topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html
    type: Tutorial
  tags:
  - single-cell
  - transcriptomics
  type: Demo
  versions:
  - link: 22t-4qvHnow
    length: 11M
    date: '2023-05-09'
    speakers:
    - hrukkudyr
    captions:
    - hrukkudyr
  - captions:
    - nomadscientist
    date: '2021-02-15'
    galaxy_version: '21.09'
    length: 11M
    link: U8pVa6csmUE # TODO: Move to the GTN account
    speakers:
    - nomadscientist

single-cell/scrna-case_cell-cycle/tutorial:
  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:
  - link: topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html
    type: Tutorial
  tags:
    - single-cell
    - transcriptomics
  versions: []
    #- link:
    #  date: '2042-4-2'
    #  galaxy_version: '23.01'
    #  length: 42H42M
    #  speakers:
    #  - MarisaJL
    #  captions:

transcriptomics/introduction/slides:
  description: RNA sequencing is used to assess the expression levels of genes. This
    video introduces the important concepts related to RNA-seq analysis.
  materials:
  - link: topics/transcriptomics/slides/introduction.html
    title: Introduction to Transcriptomics
    type: Slides
  tags:
  - transcriptomics
  type: Lecture
  versions:
  - captions:
    - nagoue
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 30M
    link: qKkS_tztw_Q
    speakers:
    - fpsom
transcriptomics/mirna-target-finder/slides:
  materials:
  - link: topics/transcriptomics/tutorials/mirna-target-finder/slides.html
    type: Slides
  tags:
  - transcriptomics
  type: Lecture
  versions:
  - captions:
    - galaxycommunity
    date: '2021-04-20'
    galaxy_version: '21.01'
    length: 10M
    link: FNmZoo2OXTU
    speakers:
    - awspolly
  - captions:
    - gallardoalba
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 10M
    link: 7t0Gr1Jklqs
    speakers:
    - awspolly
transcriptomics/mirna-target-finder/tutorial:
  materials:
  - link: topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html
    type: Tutorial
  tags:
  - transcriptomics
  type: Tutorial
  versions:
  - captions:
    - gallardoalba
    date: '2021-07-25'
    galaxy_version: '21.05'
    length: 1H10M
    link: wS1X_0Mgw7M
    speakers:
    - gallardoalba
transcriptomics/ref-based/tutorial:
  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.
  materials:
  - link: topics/transcriptomics/tutorials/ref-based/tutorial.html
    title: Reference-based RNA-Seq data analysis
    type: Tutorial
  tags:
  - transcriptomics
  type: Tutorial
  versions:
  - link: AeiW3IItO_c
    speakers:
    - lldelisle
    captions: [lldelisle]
    date: '2023-05-15'
    galaxy_version: '23.01'
    length: 2H50M
    cyoa: true
  - captions:
    - hexylena
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 2H30M
    link: j4onRSN650A
    speakers:
    - bebatut
transcriptomics/rna-seq-counts-to-viz-in-r/tutorial:
  description: In this tutorial, we will visualize our RNA-seq analysis results using
    R.
  materials:
  - link: topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.html
    title: RNA Seq Counts to Viz in R
    type: Tutorial
  tags:
  - transcriptomics
  type: Tutorial
  versions:
  - captions:
    - hexylena
    - shiltemann
    - fpsom
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 30M
    link: rJWgnLgA2BE
    speakers:
    - fpsom
transcriptomics/rna-seq-viz-with-volcanoplot-r/tutorial:
  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.
  materials:
  - link: topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot-r/tutorial.html
    title: Customizing your Volcano plots using R in Galaxy
    type: Tutorial
  support_channel: transcriptomics_rna-seq-viz-with-volcanoplot
  tags:
  - transcriptomics
  - visualisation
  type: Tutorial
  versions:
  - captions:
    - mblue9
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 15M
    link: 4dspgiwkuxk
    speakers:
    - mblue9
transcriptomics/rna-seq-viz-with-volcanoplot/tutorial:
  description: This tutorial will show you how you can create volcano plots from your
    RNA-Seq analysis results using Galaxy tools.
  materials:
  - link: topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.html
    title: Visualization of RNA-Seq results with Volcano Plot
    type: Tutorial
  tags:
  - transcriptomics
  - visualisation
  type: Tutorial
  versions:
  - captions:
    - mblue9
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 10M
    link: uNGXIcEGZwA
    speakers:
    - mblue9
single-cell/scrna-case_JUPYTER-trajectories/tutorial:
  description: "You\u2019ve 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\u2026 and you\u2019ve 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\u2019ll be able to make and interpret glorious plots even without\
    \ understanding the Python coding language. This is the beauty of Galaxy - all\
    \ the \u2018set-up\u2019 is identical across computers, because it\u2019s browser\
    \ based. So fear not!"
  materials:
  - link: topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories/tutorial.html
    type: Tutorial
  tags:
  - transcriptomics
  - single-cell
  type: Demo
  versions:
  - captions:
    - nomadscientist
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 10M
    link: VEyTmwDIgPI
    speakers:
    - nomadscientist
single-cell/scrna-intro/slides:
  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. <strong>Slides
    created by Mehmet Tekman</strong>.
  materials:
  - link: topics/single-cell/tutorials/scrna-intro/slides-plain.html
    title: An introduction to scRNA-Seq data analysis
    type: Slides
  tags:
  - transcriptomics
  - single-cell
  type: Lecture
  versions:
  - captions:
    - mtekman
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 20M
    link: D3qvYWZMFa0
    speakers:
    - awspolly
single-cell/scrna-plant/tutorial:
  description: "This tutorial replicates the paper \u201CSpatiotemporal Developmental\
    \ Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell\
    \ RNA Sequencing\u201D (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)."
  materials:
  - link: topics/single-cell/tutorials/scrna-plant/tutorial.html
    type: Tutorial
  tags:
  - transcriptomics
  - single-cell
  type: Tutorial
  versions:
  - captions:
    - mtekman
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 55M
    link: yKlJ5ESri7o
    speakers:
    - mtekman
single-cell/scrna-preprocessing-tenx/tutorial:
  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.
  materials:
  - link: topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html
    title: Pre-processing of 10X Single-Cell RNA Datasets
    type: Tutorial
  tags:
  - transcriptomics
  - single-cell
  title: Pre-processing of 10X Single-Cell RNA Datasets
  type: Demo
  versions:
  - captions:
    - khanteymoori
    date: '2021-03-18'
    galaxy_version: '21.01'
    length: 5M
    link: vNBNFkF0L4U
    speakers:
    - nomadscientist
single-cell/scrna-scanpy-pbmc3k/tutorial:
  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.
  materials:
  - link: topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html
    type: Tutorial
  tags:
  - transcriptomics
  - single-cell
  title: Clustering 3K PBMCs with Scanpy
  type: Demo
  versions:
  - captions:
    - hrhotz
    date: '2021-03-18'
    length: 45M
    link: nefB35Bi1l4
    speakers:
    - nomadscientist
single-cell/scrna-case_basic-pipeline/tutorial:
  description: "You\u2019ve 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\u2019s 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!"
  materials:
  - link: topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html
    type: Tutorial
  tags:
  - transcriptomics
  - single-cell
  type: Demo
  versions:
  - captions:
    - nomadscientist
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 30M
    link: M6iepSJh0EQ
    speakers:
    - nomadscientist
single-cell/scrna-umis/tutorial:
  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.
  materials:
  - link: topics/single-cell/tutorials/scrna-umis/tutorial.html
    type: Tutorial
  tags:
  - transcriptomics
  title: Understanding Barcodes
  type: Demo
  versions:
  - captions:
    - khanteymoori
    date: '2021-03-18'
    galaxy_version: '21.01'
    length: 10M
    link: AJ17BicjmYU
    speakers:
    - nomadscientist
variant-analysis/sars-cov-2-variant-discovery/tutorial:
  materials:
  - link: topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html
    type: Tutorial
  tags:
  - variant-analysis
  type: Tutorial
  versions:
  - link: hjlmCWQhBvI
    date: '2023-05-10'
    speakers:
    - wm75
    captions:
    - wm75
    length: 55M
  - captions:
    - hexylena
    date: '2021-08-09'
    length: 1H30M
    link: vnFQ2fR_fzw
    speakers:
    - wm75
variant-analysis/tb-variant-analysis/slides:
  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\u2019s most deadly infectious disease."
  materials:
  - external: true
    link: https://docs.google.com/presentation/d/16XTMh2fRrl73WVaezNAFWET0IIMXBv0MCI2engFtdQs/edit#slide=id.g6231f48ea2_0_34
    type: Slides
  tags:
  - variant-analysis
  type: Lecture
  versions:
  - captions:
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 20M
    link: yCC9EmLuyJg
    speakers:
    - pvanheus
variant-analysis/tb-variant-analysis/tutorial:
  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.
  materials:
  - link: topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html
    type: Tutorial
  tags:
  - variant-analysis
  type: Tutorial
  versions:
  - captions:
    - pvanheus
    - nagoue
    - hexylena
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 40M
    link: G1DmquX6Wh8
    speakers:
    - pvanheus

variant-analysis/trio-analysis/tutorial:
  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.
  materials:
  - link: topics/variant-analysis/tutorials/trio-analysis/tutorial.html
    type: Tutorial
  tags:
  - variant-analysis
  type: Tutorial
  versions:
  - link: 3OWXWOkJRqU
    speakers:
    - JasperO98
    captions: [JasperO98]
    date: '2023-05-12'
    length: 40M

visualisation/circos/slides:
  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
  materials:
  - link: topics/visualisation/tutorials/circos/slides.html
    type: Slides
  tags:
  - visualisation
  type: Lecture
  versions:
  - captions:
    - assuntad23
    - shiltemann
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 6M
    link: KCtI5KLp05k
    speakers:
    - hexylena
visualisation/circos/tutorial:
  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
  materials:
  - link: topics/visualisation/tutorials/circos/slides.html
    type: Slides
  - link: topics/visualisation/tutorials/circos/tutorial.html
    title: Visualisation with Circos
    type: Tutorial
  tags:
  - visualisation
  type: Tutorial
  versions:
  - captions:
    - beatrizserrano
    - hexylena
    - shiltemann
    - khanteymoori
    date: '2021-02-15'
    galaxy_version: '21.01'
    length: 50M
    link: tbqeUP67w-Y
    speakers:
    - hexylena
webinar/admins:
  materials:
  - external: true
    link: https://galaxyproject.org/events/webinars/
    title: View past & upcoming webinars
    type: Galaxy Webinar Page
  tags:
  - webinar
  title: Galaxy Resources for.. Admins
  type: Webinar
  versions:
  - captions: null
    date: '2021-05-12'
    length: 1H5M
    link: MdQyltMAocg
    speakers:
    - gmauro
    - lldelisle
webinar/educators:
  materials:
  - external: true
    link: https://galaxyproject.org/events/webinars/
    title: View past & upcoming webinars
    type: Galaxy Webinar Page
  tags:
  - webinar
  title: Galaxy Resources for.. Educators
  type: Webinar
  versions:
  - captions:
    - shiltemann
    date: '2021-04-28'
    length: 1H10M
    link: AXynJtPXgRQ
    speakers:
    - shiltemann
    - miaomiaozhou88
    - christinecucinotta
    - subinamehta
    - bebatut
webinar/researchers:
  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.
  materials:
  - external: true
    link: https://galaxyproject.org/events/webinars/
    title: View past & upcoming webinars
    type: Galaxy Webinar Page
  tags:
  - webinar
  title: Galaxy Resources for.. Researchers
  type: Webinar
  versions:
  - captions: null
    date: '2021-04-21'
    length: 1H10M
    link: cFN_WPGz9qk
    speakers:
    - tnabtaf
webinar/tooldevs:
  materials:
  - external: true
    link: https://galaxyproject.org/events/webinars/
    title: View past & upcoming webinars
    type: Galaxy Webinar Page
  tags:
  - webinar
  title: Galaxy Resources for.. Tool Developers
  type: Webinar
  versions:
  - captions: null
    date: '2021-05-26'
    length: 59M
    link: vx2icgaU_h0
    speakers:
    - blankenberg
    - abretaud
    - petrnovak
wetlab/miseq/demo:
  description: This video will show you the full process of sequencing a bacterial
    genome using the Oxford Nanopore MinION sequencer.
  materials: []
  tags:
  - wetlab
  title: MinION Wetlab demo
  type: Demo
  versions:
  - captions:
    - shiltemann
    date: '2021-02-15'
    length: 20M
    link: bZfEyd87xCE
    speakers:
    - miaomiaozhou88

ro-crates/intro/slides:
  description:
  materials:
  - link: https://doi.org/10.5281/zenodo.7828632
  tags: [ro-crate]
  title: An overview of the RO-Crate concept and its implementations
  type: Tutorial
  versions:
  - captions:
      - stain
    date: '2023-04-14'
    length: 17M
    link: 5GYdN5B1tc8
    speakers:
      - stain
  support_channel: ro-crate
  cover:
    link: rocrate.png
    alt: RO Crate logo
ro-crates/publishing/tutorial:
  description:
  materials:
  - link: https://www.researchobject.org/ro-crate/1.2-DRAFT/introduction.html
  - link: https://github.com/marketplace/actions/ro-crate-preview
  tags: [ro-crate]
  title: Publishing My First™ RO-Crate
  type: Tutorial
  versions: []
  support_channel: ro-crate
  cover:
    link: rocrate.png
    alt: RO Crate logo
ro-crates/python/tutorial:
  description:
  materials:
  - link: https://by-covid.github.io/gtn/ro-crate-in-python/
  tags: [ro-crate, python]
  title: RO-Crate in Python
  type: Tutorial
  versions: []
  support_channel: ro-crate
  cover:
    link: rocrate.png
    alt: RO Crate logo
ro-crates/workflow-run-crate/tutorial:
  description:
  materials:
  - link: https://by-covid.github.io/gtn/workflow-run-ro-crate/
  tags: [ro-crate]
  title: Workflow Run RO-Crate Introduction
  type: Tutorial
  versions: []
  support_channel: ro-crate
  cover:
    link: rocrate.png
    alt: RO Crate logo
ro-crates/workflowhub/tutorial:
  description:
  materials:
  - link: https://doi.org/10.5281/zenodo.7787488
  - link: https://about.workflowhub.eu/docs/registering-a-workflow/
  tags: [ro-crate, workflowhub]
  title: Registering Galaxy workflows in WorkflowHub
  type: Tutorial
  versions:
  - captions: [biocommons]
    date: '2023-03-21'
    length: 35M
    link: 2kGKxaPuQN8
    speakers:
    - supernord
  support_channel: ro-crate
  cover:
    link: rocrate.png
    alt: RO Crate logo
ro-crates/bestpractices/tutorial:
  description:
  materials:
  - link: https://by-covid.github.io/gtn/galaxy-best-practices/
  - link: https://github.com/galaxyproject/iwc/blob/main/workflows/README.md#adding-workflows
  tags: [ro-crate]
  title: Best practices for workflows in GitHub repositories
  type: Tutorial
  versions: []
  support_channel: ro-crate
  cover:
    link: rocrate.png
    alt: RO Crate logo
ro-crates/lifemonitor/tutorial:
  description:
  materials:
  - link: https://by-covid.github.io/gtn/submitting-life-monitor
  tags: [ro-crate]
  title: Submitting workflows to LifeMonitor
  type: Tutorial
  versions: []
  support_channel: ro-crate
  cover:
    link: rocrate.png
    alt: RO Crate logo

bioconductor/bioc-intro/tutorial:
  title: Introduction to data analysis with R and Bioconductor
  type: Tutorial
  instructors:
    - lgatto
  cover:
    link: bioconductor-session.jpg
    alt: Bioconductor logo
  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:
  - link: https://carpentries-incubator.github.io/bioc-intro/
    external: true
  tags: [bioconductor, r]
  support_channel: bioconductor
bioconductor/bioc-project/tutorial:
  title: The Bioconductor project
  type: Tutorial
  instructors:
    - kevinrue
  cover:
    link: bioconductor-session.jpg
    alt: Bioconductor logo
  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:
  - link: https://carpentries-incubator.github.io/bioc-project/
  tags: [bioconductor, r]
  versions: []
  support_channel: bioconductor
bioconductor/rformassspectrometry/tutorial:
  title: R for Mass Spectrometry
  type: Tutorial
  instructors:
    - lgatto
  cover:
    link: bioconductor-session.jpg
    alt: Bioconductor logo
  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:
  - link: https://rformassspectrometry.github.io/docs/
  tags: [bioconductor, r]
  versions: []
  support_channel: bioconductor
bioconductor/isee/tutorial:
  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
  materials:
  - link: https://isee.github.io/iSEEWorkshop2020/
  tags: [bioconductor, r]
  title: Interactive visualization of SummarizedExperiment objects with iSEE
  type: Tutorial
  versions:
  - captions:
    date: '2020-07-28'
    length: 55M
    link: qmoJtL8b438
    speakers:
    - csoneson
    - kevinrue
    - federicomarini
  support_channel: bioconductor
bioconductor/epiforbioworkshop2022/tutorial:
  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.
  materials:
  - link: https://chloemirzayi.com/epiforbioworkshop2022/articles/EpiForBioWorkshop.html
  tags: [bioconductor, r]
  title: Epidemiology for Bioinformaticians
  type: Tutorial
  versions:
  - captions:
    date: '2022-07-27'
    length: 83M
    link: u2ahgX823Fg
    speakers:
    - cmirzayi
  support_channel: bioconductor
bioconductor/bioc2022_tidytranscriptomics/tutorial:
  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.
  materials:
  - link: https://tidytranscriptomics-workshops.github.io/bioc2022_tidytranscriptomics/articles/tidytranscriptomics_case_study.html
  tags: [bioconductor, r]
  title: Tidy Transcriptomics For Single-Cell RNA Sequencing Analyses
  type: Tutorial
  versions:
  - captions:
    date: '2022-07-28'
    length: 1H27M
    link: LKWcut6l--c
    speakers:
    - stemangiola
  support_channel: bioconductor
bioconductor/CompGenomicsBioc2022/tutorial:
  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.
  materials:
  - link: https://www.ahl27.com/CompGenomicsBioc2022/index.html
  tags: [bioconductor, r]
  title: Comparative Genomics with DECIPHER and SynExtend
  type: Tutorial
  versions:
  - captions:
    date: '2022-07-29'
    length: 1H5M
    link: JgTc2jiMPF0
    speakers:
    - ahl27
  support_channel: bioconductor
bioconductor/fluentGenomics/tutorial:
  title: "fluentGenomics: A plyranges and tximeta workflow"
  type: Tutorial
  instructors:
    - mikelove
  cover:
    link: bioconductor-session.jpg
    alt: Bioconductor logo
  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:
  - link: https://bit.ly/fluentGenomics
  tags: [bioconductor, r]
  versions: []
  support_channel: bioconductor
bioconductor/RNAseq123/tutorial:
  title: "RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR"
  type: Tutorial
  instructors:
    - mritchie
  cover:
    link: bioconductor-session.jpg
    alt: Bioconductor logo
  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:
  - link: https://bit.ly/RNAseq123
  tags: [bioconductor, r]
  versions: []
  support_channel: bioconductor
bioconductor/RnaSeqGeneEdgeRQL/tutorial:
  title: "From reads to genes to pathways: differential expression analysis of
  RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline"
  type: Tutorial
  instructors:
    - yunshun
  cover:
    link: bioconductor-session.jpg
    alt: Bioconductor logo
  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:
  - link: https://bit.ly/RnaSeqGeneEdgeRQL
  tags: [bioconductor, r]
  versions: []
  support_channel: bioconductor
bioconductor/SingscoreAMLMutations/tutorial:
  title: Using singscore to predict mutations in AML from transcriptomic signatures
  type: Tutorial
  instructors:
    - bhuvad
  cover:
    link: bioconductor-session.jpg
    alt: Bioconductor logo
  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:
  - link: https://bit.ly/SingscoreAMLMutations
  tags: [bioconductor, r]
  versions: []
  support_channel: bioconductor