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.

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 logoAnthony Bretaudeau avatar Anthony BretaudeauAnna Trigos avatar Anna TrigosCharity Law avatar Charity Laworcid logoErwan Corre avatar Erwan Correorcid logoToby Hodges avatar Toby Hodgesorcid logoMira Kuntz avatar Mira Kuntzorcid logoCristóbal Gallardo avatar Cristóbal GallardoGildas Le Corguillé avatar Gildas Le Corguilléorcid logoMo Heydarian avatar Mo HeydarianXavier Garnier avatar Xavier Garnierorcid logoMallory Freeberg avatar Mallory Freebergorcid logoClemens Blank avatar Clemens Blankorcid logoBérénice Batut avatar Bérénice BatutAnne Siegel avatar Anne Siegelorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoLucille Delisle avatar Lucille Delisleorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoIacopo Cristoferi avatar Iacopo CristoferiChao Zhang avatar Chao Zhangorcid logoMarek Ostaszewski avatar Marek OstaszewskiJames Taylor avatar James TaylorMarkus Wolfien avatar Markus Wolfienorcid logoMatti Hoch avatar Matti HochJovana Maksimovic avatar Jovana Maksimovicorcid logoBjörn Grüning avatar Björn GrüningJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkAndrea Bagnacani avatar Andrea Bagnacaniorcid logoMaria Doyle avatar Maria Doyleorcid logoNicola Soranzo avatar Nicola SoranzoMatt Ritchie avatar Matt RitchieAnton Nekrutenko avatar Anton NekrutenkoShian Su avatar Shian Suorcid logoFlorian Heyl avatar Florian HeylIGC Bioinformatics Unit avatar IGC Bioinformatics UnitSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamHarriet Dashnow avatar Harriet Dashnoworcid logoPeter van Heusden avatar Peter van Heusdenorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoAnika Erxleben avatar Anika ErxlebenOlivier Dameron avatar Olivier DameronXi Liu avatar Xi Liuorcid logoPavankumar Videm avatar Pavankumar VidemDaniel Maticzka avatar Daniel Maticzkaorcid logoHelena Rasche avatar Helena RascheThe Carpentries avatar The Carpentriesorcid logoMateo Boudet avatar Mateo Boudetorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoBelinda Phipson avatar Belinda Phipson

Funders

This material was funded by:

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

References