Transcriptomics

Training material for all kinds of transcriptomics analysis.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

Introduction

Start here if you are new to RNA-Seq analysis in Galaxy

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Transcriptomics
Reference-based RNA-Seq data analysis
De novo transcriptome reconstruction with RNA-Seq

End-to-End Analysis

These tutorials take you from raw sequencing reads to pathway analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
1: RNA-Seq reads to counts
2: RNA-seq counts to genes
3: RNA-seq genes to pathways

Visualisation

Tutorials covering data visualisation

Lesson Slides Hands-on Recordings Input dataset Workflows
RNA Seq Counts to Viz in R
Visualization of RNA-Seq results with CummeRbund
Visualization of RNA-Seq results with Volcano Plot
Visualization of RNA-Seq results with Volcano Plot in R
Visualization of RNA-Seq results with heatmap2
Pathway analysis with the MINERVA Platform

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
CLIP-Seq data analysis from pre-processing to motif detection
Differential abundance testing of small RNAs
GO Enrichment Analysis
Genome-wide alternative splicing analysis
Network analysis with Heinz
RNA-RNA interactome data analysis
RNA-Seq analysis with AskOmics Interactive Tool
RNA-seq Alignment with STAR
Small Non-coding RNA Clustering using BlockClust
Whole transcriptome analysis of Arabidopsis thaliana

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/transcriptomics-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoBérénice Batut avatar Bérénice Batutorcid logoMaria Doyle avatar Maria Doyleorcid logoFlorian Heyl avatar Florian Heyl

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

orcid logoLucille Delisle avatar Lucille Delisleorcid logoAnthony Bretaudeau avatar Anthony BretaudeauJames Taylor avatar James TaylorBelinda Phipson avatar Belinda PhipsonHarriet Dashnow avatar Harriet Dashnoworcid logoBjörn Grüning avatar Björn GrüningIGC Bioinformatics Unit avatar IGC Bioinformatics UnitChao Zhang avatar Chao Zhangorcid logoNicola Soranzo avatar Nicola SoranzoMarkus Wolfien avatar Markus WolfienAndrea Bagnacani avatar Andrea BagnacaniCharity Law avatar Charity Laworcid logoFlorian Heyl avatar Florian Heylorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoIacopo Cristoferi avatar Iacopo CristoferiAnne Siegel avatar Anne Siegelorcid logoMarek Ostaszewski avatar Marek OstaszewskiJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoSofoklis Keisaris avatar Sofoklis KeisarisShian Su avatar Shian Suorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoMira Kuntz avatar Mira Kuntzorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoPeter van Heusden avatar Peter van HeusdenXavier Garnier avatar Xavier GarnierThe Carpentries avatar The CarpentriesMatt Ritchie avatar Matt Ritchieorcid logoAnika Erxleben avatar Anika ErxlebenJovana Maksimovic avatar Jovana Maksimovicorcid logoToby Hodges avatar Toby HodgesOlivier Dameron avatar Olivier Dameronorcid logoClemens Blank avatar Clemens BlankSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoHelena Rasche avatar Helena RascheGildas Le Corguillé avatar Gildas Le Corguilléorcid logoMatti Hoch avatar Matti HochDaniel Maticzka avatar Daniel MaticzkaAnna Trigos avatar Anna Trigosorcid logoBérénice Batut avatar Bérénice Batutorcid logoMo Heydarian avatar Mo HeydarianAnton Nekrutenko avatar Anton NekrutenkoXi Liu avatar Xi Liuorcid logoErwan Corre avatar Erwan Correorcid logoMateo Boudet avatar Mateo Boudetorcid logoMaria Doyle avatar Maria Doyle

Funders

This material was funded by:

BeYond-COVID avatar BeYond-COVIDGallantries: Bridging Training Communities in Life Science, Environment and Health avatar Gallantries

References