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training_sessions_science.yaml
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training_sessions_science.yaml
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---
intro:
title: Welcome & Practical Information
sessions:
- name: Welcome & Course Information
description: "Start here; we will go over all the important things to know to get the most out of this workshop"
speaker: shiltemann
type: Lecture
video:
link: YXEnyIvYEKo
length: 25M
captions: [shiltemann]
material:
- type: Slides
external: true
link: "https://shiltemann.github.io/presentations//2020-12-18-smorgasbord"
support_channel: "#general"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01ES8R0RNG"
faq: "https://docs.google.com/document/d/e/2PACX-1vTfNT2qS2Yb7qTAcnOFrMWwE_aPPUuYJJ0hdjw5gqV_JtMUWQ3NSkr6qAdrmF2EUGBBzTL8wFiILz8B/pub"
- name: "Get set up for the course"
type: setup
- name: "Meet & Join the Galaxy Community!"
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>."
speaker: galaxycommunity
video:
link: -1MPdxmRs8U
length: 5M
captions: [shiltemann]
material: &communitymaterial
- type: GalaxyProject Home
external: true
title: galaxyproject.org
link: "https://galaxyproject.org"
- type: Galaxy servers
external: true
title: Find a Galaxy server near you!
link: "https://galaxyproject.org/use/"
- type: Galaxy Training Network
external: true
title: Start learning Galaxy
link: "https://training.galaxyproject.org"
- type: Support
external: true
link: "https://help.galaxyproject.org/"
title: Galaxy Help Forum
- type: Galaxy Publications
external: true
title: Zotero
link: "https://www.zotero.org/groups/1732893/galaxy"
- type: Galaxy Communities
external: true
title: Find and Join a community
link: "https://galaxyproject.org/community/"
- type: Events
external: true
link: "https://galaxyproject.org/events/"
title: Galaxy Event Horizon
- type: Mailing Lists
external: true
title: Stay informed of Galaxy activity!
link: "https://galaxyproject.org/mailing-lists/"
- type: Galaxy Working Groups
external: true
link: "https://galaxyproject.org/community/wg/"
title: Find and join a WG
- type: GitHub
external: true
link: "https://github.com/galaxyproject"
title: galaxyproject
- type: Gitter Chat
external: true
link: "https://gitter.im/galaxyproject/Lobby"
title: Start talking with the Galaxy Community!
- type: GTN Gitter
external: true
title: Join the training discussion here!
link: "https://gitter.im/Galaxy-Training-Network/Lobby"
- type: PaperCuts
external: true
title: Monthly Collaboration Fest
link: "https://galaxyproject.org/events/2021-02-papercuts/"
- type: GTN CoFest
external: true
title: Everybody Welcome!
link: "https://github.com/galaxyproject/training-material/issues/1712"
- type: Twitter
external: true
title: follow @galaxyproject
link: "https://twitter.com/galaxyproject"
- type: Twitter
external: true
title: follow the GTN @gxytraining
link: "https://twitter.com/gxytraining"
galaxyintro:
title: "Introduction to Galaxy"
description: "Today we start by introducing the Galaxy Platform, and show you how to analyze your NGS data using Galaxy. Today we have a mixture of lecutres, demos, and hands-on tutorials."
sessions:
- name: "A Very Short Introduction to Galaxy"
type: Lecture/Demo
description: |
This video will introduce the Galaxy data analysis platform, and give a short demo on how to use it.
speaker: nekrut
video:
link: VZoz3k5EehI
length: 10M
captions: [nekrut]
material:
- type: Slides
link: topics/introduction/videos/
title: A Slightly Longer Introduction to Galaxy
support_channel: "#1-1_galaxy-intro"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01ES914GCU"
faq: "https://docs.google.com/document/d/e/2PACX-1vQ1SZCsxEcRXp39J2BcFAjXyC3B20sWzI7IVgBgwe2pcC9b0cza417jzBPYJVqCRNbU0dD4rv_y6u6P/pub"
- name: "A Longer Introduction to Galaxy"
type: Tutorial
description: This video tutorial will provide a very first look at the Galaxy platform, how to use it, and discusses how you can get support for your data analysis.
speaker: jennaj
video:
link:
length:
captions:
material:
- type: Tutorial
link: topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html
- name: "Galaxy 101 for Everyone"
type: 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.
speaker: annefou
video:
link:
length:
captions:
material:
- type: Tutorial
link: topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html
- name: "Your First Galaxy Analysis"
type: Tutorial
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.
speaker: tnabtaf
video:
link: 1UPCrQxGwcU
length: 1H30M
captions: [tnabtaf]
material:
- type: Slides
link: "https://docs.google.com/presentation/d/1rOGp4o_Dc-QIHS4YT4HizdfXTVhJB1HwPPZkSDuMhig/edit#slide=id.gbc9627d000_0_346"
external: true
title: Overview Prsentations
- type: Tutorial
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
support_channel: "#1-1_galaxy-intro"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01ES914GCU"
faq: "https://docs.google.com/document/d/e/2PACX-1vQ1SZCsxEcRXp39J2BcFAjXyC3B20sWzI7IVgBgwe2pcC9b0cza417jzBPYJVqCRNbU0dD4rv_y6u6P/pub"
ngsintro:
title: Introduction to NGS Analysis
description: This module will introduce the basics of NGS analysis, from cleaning your data to mapping and assembly
sessions:
- name: "Demo: NGS Data Logistics using SARS-CoV-2 data"
type: Demo
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).
speaker: nekrut
video:
link: 9mIL0tIfZ_o
length: 15M
captions: [nekrut]
material:
- type: Tutorial
link: topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html
support_channel: "#1-2_ngs-intro"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01EXB3BKN1"
faq: "https://docs.google.com/document/u/2/d/12w_KCVN7z9DKLSxX6aCRfr8__nfANoIxfLJeYM4UGQA/pub"
- name: "Quality Control: Intro"
speaker: heylf
type: Lecture
description: |
This tutorial covers the basics about how to assess and improve the quality of your sequencing data.
video:
link: BWonTPS4zB8
length: 40M
captions: [ennovytje,nagoue,hexylena]
material:
- type: Slides
link: topics/sequence-analysis/tutorials/quality-control/slides.html
title: Introduction to Quality Control
support_channel: "#1-3_quality-control"
support_link: https://gtnsmrgsbord.slack.com/archives/C01FQ92MB7A
faq: "https://docs.google.com/document/d/e/2PACX-1vRXhvMQNVRc41Xsg7NLeCLSefaWMEhKgkENmqQqAJUfZAk782616svDQPBQhMKeOqMhiKSZDbmFqsfO/pub"
- name: "Quality Control: Hands-on!"
type: Tutorial
speaker: heylf
description: |
Get hands-on experience assessing and improving the quality of
your sequencing data in Galaxy.
video:
link: QJRlX2hWDKM
length: 1H10M
captions: [bebatut,nagoue,shiltemann]
material:
- type: Tutorial
link: "topics/sequence-analysis/tutorials/quality-control/tutorial.html"
support_channel: "#1-3_quality-control"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01FQ92MB7A"
faq: "https://docs.google.com/document/d/e/2PACX-1vRXhvMQNVRc41Xsg7NLeCLSefaWMEhKgkENmqQqAJUfZAk782616svDQPBQhMKeOqMhiKSZDbmFqsfO/pub"
- name: "Mapping: Introduction"
type: Lecture
speaker: pvanheus
description: |
Mapping sequencing reads to a reference genome is often the next step
after QC. This session covers the basic concepts of mapping.
video:
link: 7FhHb8EV3EU
length: 10M
captions: [blankenberg]
material:
- type: Slides
link: topics/sequence-analysis/tutorials/mapping/slides.html
title: Mapping
support_channel: "#1-4_mapping"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01F6JHCFT6"
faq: "https://docs.google.com/document/d/e/2PACX-1vReZf8DGTSf6DlgBzg_g4_PhiH7glzRNTXGxK2_xM3aAFL5A3x0FdawNCrna3NkZ_vj986u7nhWh3Bb/pub"
- name: "Mapping: Hands-on!"
type: Tutorial
speaker: pvanheus
description: |
In this tutorial you will map sequencing data to a reference genome,
and explore the mapped reads in a genome browser.
video:
link: 1wm-62E2NkY
length: 20M
captions: [shiltemann]
material:
- type: Tutorial
link: topics/sequence-analysis/tutorials/mapping/tutorial.html
title: Mapping
support_channel: "#1-4_mapping"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01F6JHCFT6"
faq: "https://docs.google.com/document/d/e/2PACX-1vReZf8DGTSf6DlgBzg_g4_PhiH7glzRNTXGxK2_xM3aAFL5A3x0FdawNCrna3NkZ_vj986u7nhWh3Bb/pub"
- name: "Genome Assembly: Introduction"
description: |
When there is no reference genome available for your organism, you will
have to assemble the short reads into larger segments (contigs). This
introduction covers the basics of this assembly process.
type: Lecture
speaker: slugger70
video:
link: -EX_G1griZE
length: 25M
captions: [shiltemann, hexylena]
material:
- type: Slides
link: topics/assembly/tutorials/general-introduction/slides.html
title: An Introduction to Genome Assembly
support_channel: "#1-5_assembly"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01EKMD8VC7"
faq: "https://docs.google.com/document/d/e/2PACX-1vTed-1_nZK1liUdm5IZn_Qas7LcJE700WwsMAgT282Q1jx0Nkk4lZzzN47P9aS1suUAeh0ljIUYgXpG/pub"
- name: "Genome Assembly: Hands-on!"
type: Tutorial
description: |
In this tutorial, you will assemble a chloroplast genome using a
combination of short and long read data.
speaker: annasyme
video:
link: eyfCyINTD_E
length: 35M
captions: [annasyme]
material:
- type: Tutorial
link: topics/assembly/tutorials/chloroplast-assembly/tutorial.html
title: Chloroplast genome assembly
support_channel: "#1-5_assembly"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01EKMD8VC7"
faq: "https://docs.google.com/document/d/e/2PACX-1vTed-1_nZK1liUdm5IZn_Qas7LcJE700WwsMAgT282Q1jx0Nkk4lZzzN47P9aS1suUAeh0ljIUYgXpG/pub"
ngsadvanced:
title: "Advanced NGS Analysis"
sessions:
- name: "Assembly: Unicycler assembly of SARS-CoV-2 genome"
speaker: gallardoalba
type: Tutorial
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."
video:
link: jNFLYhjgJPs
length: 25M
captions: [mtekman]
material:
- type: Slides
link: topics/assembly/tutorials/assembly-with-preprocessing/slides.html
- type: Tutorial
link: topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html
support_channel: "#5-h_unicycler-assembly-sars-cov2-genome"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01GJLDS01K"
faq: "https://docs.google.com/document/d/e/2PACX-1vRcBWHbIIo6t_vXtZiaW_6t2qIUYwjiptC2MRVUG5KC31rwPg8fO9yCma22HqIV6Hu1T3wJXaV-GwxU/pub"
- name: "Genome Annotation: Annotation of a prokaryotic genome: Slides"
speaker: awspolly
type: Lecture
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."
video:
link: eqHy-Cc7k4Q
length: 3M
captions: [abretaud]
material:
- type: Tutorial
link: topics/genome-annotation/tutorials/annotation-with-prokka/slides.html
support_channel: "#5-g_annotation-prokaryotic-genome"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01GTTD1BE0"
faq: "https://docs.google.com/document/d/e/2PACX-1vSK-RjeRJC38_FSM9zC6SrfkvIz1W4uEMQkN95qk5OemvANuPF3aNEogVEvF6JEXeMomo-oMwi32Gv2/pub"
- name: "Genome Annotation: Annotation of a prokaryotic genome: Hands-on!"
speaker: abretaud
type: 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."
video:
link: B8pIQZPf21Y
length: 20M
captions: [abretaud]
material:
- type: Tutorial
link: topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html
- type: Slides
link: topics/genome-annotation/videos/
support_channel: "#5-g_annotation-prokaryotic-genome"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01GTTD1BE0"
faq: "https://docs.google.com/document/d/e/2PACX-1vSK-RjeRJC38_FSM9zC6SrfkvIz1W4uEMQkN95qk5OemvANuPF3aNEogVEvF6JEXeMomo-oMwi32Gv2/pub"
- name: "Genome Annotation with Apollo"
speaker: abretaud
type: Tutorial
video:
link: B8pIQZPf21Y
length: 20M
captions: [abretaud]
- name: "Epigenetics: ATAC-Seq data analysis"
type: Tutorial
speaker:
instructors: [hrhotz, lldelisle, heylf]
description: "In many eukaryotic organisms, such as humans, the genome is tightly packed and organized with the help of nucleosomes (chromatin). A nucleosome is a complex formed by eight histone proteins that is wrapped with ~147bp of DNA. When the DNA is being actively transcribed into RNA, the DNA will be opened and loosened from the nucleosome complex. Many factors, such as the chromatin structure, the position of the nucleosomes, and histone modifications, play an important role in the organization and accessibility of the DNA. Consequently, these factors are also important for the activation and inactivation of genes. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq) is a method to investigate the accessibility of chromatin and thus a method to determine regulatory mechanisms of gene expression. The method can help identify promoter regions and potential enhancers and silencers. "
video:
link:
length:
captions:
material:
- type: Tutorial
link: topics/epigenetics/tutorials/atac-seq/tutorial.html
title: ATAC-Seq data analysis
support_channel: "#5-k_atac-seq"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01LRHRC6A3"
faq: "https://docs.google.com/document/d/e/2PACX-1vQnEmZyZF3rLhU3mA-g5L8DVaTW8GHYTikxYnuvQG7sCT66owCIc-4KLLGw9S2nIo1XPPtV9Ledtm3n/pub"
- name: "SRA Aligned Read Formats to Speed Up Analysis"
type: tutorial
speaker: prodromus
description: |
Traditionally, after a list of run accessions has been filtered on the NCBI website, the accessions are used to download and extract fastq using the SRA toolkit to enter into the next steps of the workflow. A newer compressed data type generated from raw submission data for sequences containing hits to SARS-CoV-2 is also accessible to Galaxy users from SRA in the Cloud.
SRA Aligned Read Format (SARFs) provides further output options other than basic fastq format, for example:
1. contigs created from the raw reads in the run (fasta format)
2. reads aligned back to the contigs (sam format)
3. VCF files generated for each record relative to the SARS-CoV-2 RefSeq record
We will demonstrate how to access just the reads (fasta or fastq format), just the contigs, the reads aligned to the contigs and vcf files for selected SARFs.
- These formats can speed up workflows such as assembly and variant calling.
- This data format is still referenced by the run accession and accessed using the SRA toolkit.
- This workshop describes the SARF data objects and demonstrates a few ways to filter them using the metadata before accessing them and entering them into Galaxy workflows.
Questions that will be answered in this workshop
- How can I search SRA SARS-CoV-2 metadata from within Galaxy?
- How can I import SRA aligned read files and extract the data in my format of choice?
- How can I import vcf files into Galaxy that have been generated for these runs?
Learning Objectives
- Learn about SRA aligned read format and VCF files for runs containing SARS-CoV-2 content.
- Understand how to search the SRA metadata for these runs to find your dataset of interest and then import that data in your preferred format.
Helpful References for SRA on Galaxy: [Tutorial on SRA Toolkit in Galaxy](https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html)
video:
link:
length:
captions:
day2:
title: "RNA-Seq"
description: "The following module cover RNA-Seq analysis in Galaxy, from bulk RNA-seq to Single-cell RNA-Seq, from Quality control to Visualisation"
rnabasics:
title: "Introduction to RNA-Seq"
subday: true
sessions:
- name: "Introduction to RNA-Seq"
type: Lecture
speaker: fpsom
description: RNA sequencing is used to assess the expression levels of genes. This video introduces the important concepts related to RNA-seq analysis.
video:
link: qKkS_tztw_Q
length: 30M
captions: [nagoue,shiltemann]
material:
- type: Slides
link: topics/transcriptomics/slides/introduction.html
title: Introduction to Transcriptomics
support_channel: "#2-1_ref-based-rna-seq"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01F0L6UW03"
faq: "https://docs.google.com/document/d/e/2PACX-1vTOAKhYdmiiTucIarwlehmnPaxi0MXDmuCPdyZwB27xvBJPksDOLCOYMGdtEZAoz4WGxHGdDcBDdlM9/pub"
- name: Reference-based RNA-seq Analysis
type: Tutorial
speaker: bebatut
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.
video:
link: j4onRSN650A # old one was 37Tc1xnrHK4
length: 2H30M
captions: [hexylena,shiltemann]
material:
- type: Tutorial
link: topics/transcriptomics/tutorials/ref-based/tutorial.html
title: Reference-based RNA-Seq data analysis
support_channel: "#2-1_ref-based-rna-seq"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01F0L6UW03"
faq: "https://docs.google.com/document/d/e/2PACX-1vTOAKhYdmiiTucIarwlehmnPaxi0MXDmuCPdyZwB27xvBJPksDOLCOYMGdtEZAoz4WGxHGdDcBDdlM9/pub"
- name: De novo transcriptome reconstruction with RNA-Seq
type: Tutorial
speaker: malloryfreeberg
description:
video:
link:
length:
captions:
material:
- type: Tutorial
link: topics/transcriptomics/tutorials/de-novo/tutorial.html
- name: Plant transcriptome analysis
type: tutorial
speaker: gallardoalba
description: In this tutorial, we will analyze RNA sequencing data to extract information about potential genes regulated in response to abiotic stress in plants. For this purpose, the chosen approach is the identification of genes with complementary regions to miRNAs upregulated in response to brassinosteroids.
video:
link:
length:
captions:
material:
- type: Tutorial
link: topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html
title: Whole transcriptome analysis of Arabidopsis thaliana
support_channel: "#plants-2-2_mirna-data-analysis"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01TCB1J7SA"
faq: ""
rnaseqandr:
title: RNA-Seq analysis using Rstudio in Galaxy
description:
subday: true
sessions:
- name: "Starting Rstudio in Galaxy"
type: Demo
speaker: fpsom
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>"
video:
link: vN14K74nFZc
length: 20M
captions: [shiltemann]
support_channel: "#2-2_intro-to-r"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01F6JXPZM2"
faq: "https://docs.google.com/document/d/e/2PACX-1vQuOJPPP2nosMG1gh1TuAFu479F4u2kGCCsICHuKvQE7lJGZCreVbXMQrhEORu3O1fV2hX_DZDE_Isk/pub"
- name: "Introduction to R"
type: Tutorial
speaker: fpsom
description: This tutorial will provide an introduction to using R with Rstudio in Galaxy.
video:
link: MKkQDh5Nguc
length: 50M
captions: [s3by01,annefou,kxk302]
material:
- type: Tutorial
link: topics/introduction/tutorials/r-basics/tutorial.html
title: R basics in Galaxy
support_channel: "#2-2_intro-to-r"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01F6JXPZM2"
faq: "https://docs.google.com/document/d/e/2PACX-1vQuOJPPP2nosMG1gh1TuAFu479F4u2kGCCsICHuKvQE7lJGZCreVbXMQrhEORu3O1fV2hX_DZDE_Isk/pub"
- name: "Advanced R in Galaxy"
type: Tutorial
speaker: fpsom
description: An advanced tutorial covering downstream analysis of RNA-seq data using R.
video:
link: _hWBGdlICqg
length: 1H
captions: [ksuderman, nagoue]
material:
- type: Tutorial
link: topics/introduction/tutorials/r-advanced/tutorial.html
title: Advanced R in Galaxy
support_channel: "#2-3_advanced_r"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01LKGNPE5V"
faq: "https://docs.google.com/document/d/e/2PACX-1vQuOJPPP2nosMG1gh1TuAFu479F4u2kGCCsICHuKvQE7lJGZCreVbXMQrhEORu3O1fV2hX_DZDE_Isk/pub"
- name: "Visualisation: RNASeq postprocessing with R"
type: Tutorial
speaker: fpsom
description: In this tutorial, we will visualize our RNA-seq analysis results using R.
video:
link: rJWgnLgA2BE
length: 30M
captions: [hexylena, shiltemann, fpsom]
material:
- type: Tutorial
link: topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.html
title: RNA Seq Counts to Viz in R
support_channel: "#2-4_visualisation-with-r"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01FD3AFLN5"
faq: "https://docs.google.com/document/d/e/2PACX-1vTRNzQHT9qyPr9kdWOM1l8HiD0A1xCRMW7bYnUCcLYmF5yJFytYSOVrq_JFtRvqnat-_41JBkQray2F/pub"
rnaseqsinglecell:
title: "Single-cell RNA-Seq Analysis"
subday: true
sessions:
- name: "An introduction to scRNA-seq data analysis"
speaker: awspolly
type: Lecture
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>.
video:
link: D3qvYWZMFa0
length: 20M
captions: [mtekman]
material:
- type: Slides
link: topics/transcriptomics/tutorials/scrna-intro/slides.html
title: An introduction to scRNA-Seq data analysis
support_channel: "#3-0_single-cell-rnaseq"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01M17R4YA1"
faq: "https://docs.google.com/document/d/e/2PACX-1vSVFOV1C6hqMPGIpZ1qeOo6t-ubjaWbtsGSTMH9TwNlvfqZrP48i0_7_Xk5rxmY7g2CroOF1dNIyfMY/pub"
- name: "Understanding Barcodes"
speaker: nomadscientist
type: Demo
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.
video:
link: AJ17BicjmYU
length: 10M
captions: [khanteymoori]
material:
- type: Tutorial
link: topics/transcriptomics/tutorials/scrna-umis/tutorial.html
title: Understanding Barcodes
support_channel: "#3-1_understanding-barcodes"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01EXBNDKT7"
faq: "https://docs.google.com/document/d/e/2PACX-1vRWe-8VHsJ4vbO8rwXemPDKUabWrKy1NRnxOKfIzEgj8RQ0tfG0W1kyUx30gVyWND_h4s12MtsV58Sh/pub"
- name: "Pre-processing of 10X Single-Cell RNA Datasets"
speaker: nomadscientist
type: Demo
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.
video:
link: vNBNFkF0L4U
length: 5M
captions: [khanteymoori]
material:
- type: Tutorial
link: topics/transcriptomics/tutorials/scrna-preprocessing-tenx/tutorial.html
title: Pre-processing of 10X Single-Cell RNA Datasets
support_channel: "#3-2_preprocessing-10x-single-cell-rna-datasets"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01EXBPPBK7"
faq: "https://docs.google.com/document/d/e/2PACX-1vTuCzmNJlZSbS9-lIdfLgt8T7IJb7jWZ3gedtjNB4aKJ7pAi3apYS4NgfaCRh0_r5QbF4Pwl15Z0-mk/pub"
- name: "Clustering 3K PBMCs with Scanpy"
speaker: nomadscientist
type: Demo
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."
video:
link: nefB35Bi1l4
length: 45M
captions: [hrhotz]
material:
- type: Tutorial
link: topics/transcriptomics/tutorials/scrna-scanpy-pbmc3k/tutorial.html
title: Clustering 3K PBMCs with Scanpy
support_channel: "#3-3_clustering-3k-pbmcs-with-scanpy"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01FQ9RLLF2"
faq: "https://docs.google.com/document/d/e/2PACX-1vTdqGjslXMxUjyjqwkNtidsXFl6SRULFKFug_2TYBl-dYXIDEnXb59nMyZ5qJc6bXI-fP5cPLfkXbHV/pub"
proteomics:
title: "Proteomics"
description: In this module we explore the world of proteomics! Today we have a mixture of lectures, hands-on tutorials, and workflow demonstrations. The FAQ document provides links to example histories if you would like to explore the outputs of the demos yourself.
sessions:
- name: "Introduction to mass spectrometry based proteomics data analysis"
speaker: awspolly
instructors: foellmelanie
type: Lecture
description: This lecture will provide an introduction to mass spectrometry (MS) based proteomics analysis. <strong>Slides created by Melanie Föll</strong>.
video:
link: 2C96AvrFT38
length: 20M
captions: [foellmelanie]
material:
- type: Slides
link: topics/proteomics/slides/introduction.html
title: Introduction to proteomics, protein identification, quantification and statistical modelling
support_channel: "#4-0_introduction-to-ms-proteomics"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01MQEDM39P"
faq: "https://docs.google.com/document/d/e/2PACX-1vSYkfAT8PgEygCcqVhjzhioS23I1Tod0V2l6q60fbMkl6t21y09I62BYFrlWaSMO8p5_Y2JwilHSP5m/pub"
- name: "Maxquant + MSstats on a clinical cohort"
speaker: foellmelanie
description: "Modern mass spectrometry-based proteomics enables the identification and quantification of thousands of proteins. Therefore, quantitative mass spectrometry represents an indispensable technology for biological and clinical research. Statistical analyses are required for the unbiased answering of scientific questions and to uncover all important information in the proteomic data. In this training we will cover the full analysis workflow from label-free, data dependent acquisition (DDA) raw data to statistical results. We’ll use two popular quantitative proteomics software: MaxQuant and MSstats."
type: Tutorial
video:
link: ad3E4VaTp7M
length: 1H15M
captions: [shiltemann]
material:
- type: Tutorial
link: topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html
title: MaxQuant and MSstats for the analysis of label-free data
support_channel: "#4-1_maxquant-and-msstats"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01F0LY58R1"
faq: "https://docs.google.com/document/d/e/2PACX-1vS4GuHPJrRcpGmNCXBTJ9wyUp6X33Xe6Ou8N_q0Ko5AJ-_rUy7ZsAu-x6R9yf7iRZLxK-t_e-O4Xoc6/pub"
- name: "DIA Mass-spectrometry with EncyclopeDIA"
speaker:
instructors: [subinamehta, pratikdjagtap, timothygriffin, jj-umn, emmaleith, andrewr]
video:
link:
length:
captions:
- name: "Introduction to Proteogenomics"
speaker: timothygriffin
instructors: [subinamehta, pratikdjagtap, jj-umn, emmaleith, andrewr]
type: Lecture
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.
video:
link: WpH101OPrG0
length: 20M
captions: [emmaleith]
material:
- type: Slides
link: "https://drive.google.com/file/d/1rqzf6Mrk9cMuQ2531tM6RpltPLrDCrgh/view?usp=sharing"
external: true
support_channel: "#4-2_protegenomics"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01ETNTP6HL"
faq: "https://docs.google.com/document/d/e/2PACX-1vTjQFq5wdkZeEFiQq-E8DkOTlLI9PChgWrwekHjPYBqndlb6kuAoXDiuiJaX5N09r63dWTyLPnnL8BK/pub"
- name: "Proteogenomics 1: Database Creation"
speaker: jj-umn
instructors: [subinamehta, pratikdjagtap, timothygriffin, emmaleith, andrewr]
type: 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.
video:
link: b_kZf8mXHdo
length: 40M
captions: [emmaleith]
material:
- type: Tutorial
link: topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html
support_channel: "#4-2_protegenomics"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01ETNTP6HL"
faq: "https://docs.google.com/document/d/e/2PACX-1vTjQFq5wdkZeEFiQq-E8DkOTlLI9PChgWrwekHjPYBqndlb6kuAoXDiuiJaX5N09r63dWTyLPnnL8BK/pub"
- name: "Proteogenomics 2: Database search"
speaker: andrewr
instructors: [subinamehta, pratikdjagtap, timothygriffin, jj-umn, emmaleith]
type: Demo
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>
video:
link: q1OjmTcbvBA
length: 30M
captions: [emmaleith]
material:
- type: Tutorial
link: topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html
- type: Slides
link: "https://docs.google.com/presentation/d/1gAOJ7WQI1CEc3VeSm_fcvjg_GTxTCZ1N/edit#slide=id.p2"
external: true
support_channel: "#4-2_protegenomics"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01ETNTP6HL"
faq: "https://docs.google.com/document/d/e/2PACX-1vTjQFq5wdkZeEFiQq-E8DkOTlLI9PChgWrwekHjPYBqndlb6kuAoXDiuiJaX5N09r63dWTyLPnnL8BK/pub"
- name: "Proteogenomics 3: Novel peptide analysis"
speaker: subinamehta
instructors: [pratikdjagtap, timothygriffin, jj-umn, emmaleith, andrewr]
type: Demo
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>
video:
link: Ku274KwFh1Y
length: 40M
captions: [subinamehta]
material:
- type: Tutorial
link: topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html
support_channel: "#4-2_protegenomics"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01ETNTP6HL"
faq: "https://docs.google.com/document/d/e/2PACX-1vTjQFq5wdkZeEFiQq-E8DkOTlLI9PChgWrwekHjPYBqndlb6kuAoXDiuiJaX5N09r63dWTyLPnnL8BK/pub"
- name: "ProteoRE tool for Functional Analysis of a Protein List"
speaker: yvesvdb
type: Tutorial
description: "This tutorial covers an annotation pipeline for a protein list identified by LC-MS/MS experiments."
video:
link: qG7GZc6BeGY
length: 30M
captions: [combesf]
material:
- type: Tutorial
link: topics/proteomics/tutorials/proteome_annotation/tutorial.html
title: Annotating a protein list identified by LC-MS/MS experiments
support_channel: "#5-i_proteore-protein-list-annotation"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01EYBNQRL5"
faq: "https://docs.google.com/document/d/e/2PACX-1vT7_ulDI8Mf4BpE8JPmvXYVqk1UmMGEFJ6Cj2ZvlxwLfP8riaaVicPtGR5HeFDAEmKMjaXPcub6cL1w/pub"
- name: "ProteoRE tool for biomarker discovery"
speaker: [yvesvdb]
instructors: [yvesvdb,comesf]
type: Tutorial
description: "A biomarker is a measurable biological component that can be routinely detected in clinical practice and reflects a disease state, response to therapeutic treatment, or other relevant biological state. In this tutorial we introduce successively the tools of this pipeline, and guide you to execute them in order to complete the entire pipeline on a concrete example."
material:
- type: Tutorial
link: topics/proteomics/tutorials/biomarker_selection/tutorial.html
title: Biomarker candidate identification
support_channel: "#5-j_proteore-biomarkers-discovery"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01FP2AHUV9"
faq: "https://docs.google.com/document/d/e/2PACX-1vQVj92upQT2Z4B6ZF6kmhrbnHesbkS--e5ge14iRbxDsxRHuOb52XJE8DI584asA0t2GJIjS_qliPZu/pub"
- name: "Annotation and GO enrichment analysis of differentially expressed proteins"
speaker: yvesvdb
instructors: [yvesvdb,comesf]
type: Tutorial
video:
link:
length:
captions:
- &metaproteomics1
name: "Metaproteomics Introduction"
speaker: pratikdjagtap
instructors: [subinamehta, timothygriffin, jj-umn, emmaleith, andrewr]
type: 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.
video:
link: 3_yaPp-RCFw
length: 1H
captions: [emmaleith]
material:
- type: Tutorial
link: topics/proteomics/tutorials/metaproteomics/tutorial.html
support_channel: "#4-3_metaproteomics"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01FD4276P3"
faq: "https://docs.google.com/document/d/e/2PACX-1vTX6JQG4oAKXvQSJU52thudorwANPtzIedTiTQU1NbXQYYfrNkBheN-gHu0O91bCOIk5wQBpH1mIk7v/pub"
- &metaproteomics2
name: "Metaproteomics Analysis of COVID-19 Data"
speaker: pratikdjagtap
instructors: [subinamehta, timothygriffin, jj-umn, emmaleith, andrewr]
type: Tutorial
description: TODO
video:
link:
length:
captions:
material:
support_channel: "#4-3_metaproteomics"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01FD4276P3"
faq: "https://docs.google.com/document/d/e/2PACX-1vTX6JQG4oAKXvQSJU52thudorwANPtzIedTiTQU1NbXQYYfrNkBheN-gHu0O91bCOIk5wQBpH1mIk7v/pub"
microbial:
title: Microbial Analysis using Galaxy
sessions:
- name: "Variant Analysis: M. Tuberculosis Variant Analysis (Lecture)"
speaker: pvanheus
type: Lecture
description: "Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, in 2018 there were 10.0 million new cases of TB worldwide and 1.4 million deaths due to the disease, making TB the world’s most deadly infectious disease."
video:
link: yCC9EmLuyJg
length: 20M
captions: [shiltemann]
material:
- type: Slides
link: "https://docs.google.com/presentation/d/16XTMh2fRrl73WVaezNAFWET0IIMXBv0MCI2engFtdQs/edit#slide=id.g6231f48ea2_0_34"
external: true
support_channel: "#5-n_tuberculosis-variant-analysis"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01FD2WJU01"
faq: "https://docs.google.com/document/d/e/2PACX-1vTr2X-W-2-gronZbeEqj8OGTLyLqaUW2_7mCsHHgVMAVsOQt2faSNk5IaizQlYE_0vWU26v79Oqhyy3/pub"
- name: "Variant Analysis: M. Tuberculosis Variant Analysis (Hands-on!)"
speaker: pvanheus
type: Tutorial
description: "Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, in 2018 there were 10.0 million new cases of TB worldwide and 1.4 million deaths due to the disease, making TB the world’s most deadly infectious disease. 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."
video:
link: G1DmquX6Wh8
length: 40M
captions: [pvanheus,nagoue,hexylena]
material:
- type: Tutorial
link: topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html
support_channel: "#5-n_tuberculosis-variant-analysis"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01FD2WJU01"
faq: "https://docs.google.com/document/d/e/2PACX-1vTr2X-W-2-gronZbeEqj8OGTLyLqaUW2_7mCsHHgVMAVsOQt2faSNk5IaizQlYE_0vWU26v79Oqhyy3/pub"
- name: "Metagenomics: 16S Microbial Analysis with mothur (Lecture)"
speaker: shiltemann
type: Lecture
description: This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.
video:
link: 9OY1mklWuK0
length: 15M
captions: [shiltemann]
material:
- type: Tutorial
link: topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html
support_channel: "#5-b_16s-microbial-analysis"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01FDV16V25"
faq: "https://docs.google.com/document/d/e/2PACX-1vRPPYdMfIA9R_w5y__jV9qdKbijJyOJiclx-2ACKFkAH8aIdlU3pY84xhivWEOmeEn_XQv8StFcjDLP/pub"
- name: "Metagenomics: 16S Microbial Analysis with mothur (Hands-on!)"
speaker: shiltemann
type: Tutorial
description: In this tutorial you will perform the mothur MiSeq SOP (Standard Operating Procedure) in Galaxy.
video:
link: mto4Nl-q7Kk
length: 1H40M
captions: [shiltemann]
material:
- type: Tutorial
link: topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html
support_channel: "#5-b_16s-microbial-analysis"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01FDV16V25"
faq: "https://docs.google.com/document/d/e/2PACX-1vRPPYdMfIA9R_w5y__jV9qdKbijJyOJiclx-2ACKFkAH8aIdlU3pY84xhivWEOmeEn_XQv8StFcjDLP/pub"
- name: "Metagenomics Wetlab Demo: Genomic DNA sequencing by Oxford Nanopore MinIon"
speaker: miaomiaozhou88
type: Demo
description: "This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer."
video:
link: bZfEyd87xCE
length: 20M
captions: [shiltemann]
support_channel: "#5-a_antibiotic-resistance-detection-nanopore"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01F1GJ7JJX"
faq: "https://docs.google.com/document/d/e/2PACX-1vQlG_Onq011MQqyIu4D_erDqiLKAMLnduhHr5cDWwbXVqlU9VZhmm4OT_zphKqb8TEZprAFo8rdPXjO/pub"
- name: "Metagenomics in the Clinic: Nanopore Whole Bacterial Genome Sequencing"
speaker: aheikema
type: Lecture
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.
video:
link: icXMqMut6PY
length: 30M
captions: [hexylena]
material:
- type: Tutorial
link: topics/metagenomics/tutorials/nanopore-16S-metagenomics/tutorial.html
support_channel: "#5-a_antibiotic-resistance-detection-nanopore"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01F1GJ7JJX"
faq: "https://docs.google.com/document/d/e/2PACX-1vQlG_Onq011MQqyIu4D_erDqiLKAMLnduhHr5cDWwbXVqlU9VZhmm4OT_zphKqb8TEZprAFo8rdPXjO/pub"
- name: "Metagenomics: Antibiotic Resistance Detection with Nanopore Data"
speaker: willemdek11
type: 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.
video:
link: ECIl8ZU1Wko
length: 45M
captions: [bebatut]
material:
- type: Tutorial
link: topics/metagenomics/tutorials/plasmid-metagenomics-nanopore/tutorial.html
support_channel: "#5-a_antibiotic-resistance-detection-nanopore"
support_link: "https://gtnsmrgsbord.slack.com/archives/C01F1GJ7JJX"
faq: "https://docs.google.com/document/d/e/2PACX-1vQlG_Onq011MQqyIu4D_erDqiLKAMLnduhHr5cDWwbXVqlU9VZhmm4OT_zphKqb8TEZprAFo8rdPXjO/pub"
- name: "Metatranscriptomics analysis using microbiome RNA-seq data"
speaker: subinamehta
type: Tutorial
video:
link:
length:
captions:
material:
- type: Slides
link: topics/metagenomics/tutorials/metatranscriptomics/slides.html
title: Introduction to Metatranscrtiptomics
- type: Tutorial
link: topics/metagenomics/tutorials/metatranscriptomics/tutorial.html
- *metaproteomics1
- *metaproteomics2
machinelearning:
title: Machine Learning
description:
sessions:
- name: "Introduction to Machine Learning"
speaker: anuprulez
video:
link:
length:
captions:
- name: "Classification in Machine Learning"
speaker: anuprulez
type: Tutorial
video:
link:
length:
captions:
material:
- type: tutorial
link: topics/statistics/tutorials/classification_machinelearning/tutorial.html
- name: "Regression in Machine Learning"
speaker: anuprulez
video:
link:
length:
captions:
material:
- type: tutorial
link: topics/statistics/tutorials/regression_machinelearning/tutorial.html
- name: "Machine Learning using R in Galaxy"
speaker: fpsom
video:
link:
length:
captions: