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:

Harriet Dashnow avatar Harriet DashnowChao Zhang avatar Chao Zhangorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoMatti Hoch avatar Matti Hochorcid logoAnika Erxleben avatar Anika ErxlebenThe Carpentries avatar The Carpentriesorcid logoToby Hodges avatar Toby Hodgesorcid logoBérénice Batut avatar Bérénice BatutJosé Manuel Domínguez avatar José Manuel DomínguezGildas Le Corguillé avatar Gildas Le Corguilléorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoFlorian Heyl avatar Florian Heylorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMo Heydarian avatar Mo HeydarianOlivier Dameron avatar Olivier Dameronorcid logoBjörn Grüning avatar Björn GrüningMatt Ritchie avatar Matt Ritchieorcid logoClemens Blank avatar Clemens Blankorcid logoMaria Doyle avatar Maria DoyleIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoLucille Delisle avatar Lucille Delisleorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoMateo Boudet avatar Mateo Boudetorcid logoCristóbal Gallardo avatar Cristóbal GallardoAnna Trigos avatar Anna TrigosAnton Nekrutenko avatar Anton NekrutenkoShian Su avatar Shian SuAnne Siegel avatar Anne Siegelorcid logoPeter van Heusden avatar Peter van HeusdenMarkus Wolfien avatar Markus Wolfienorcid logoHelena Rasche avatar Helena Rascheorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosAndrea Bagnacani avatar Andrea BagnacaniXi Liu avatar Xi LiuJames Taylor avatar James Taylororcid logoMarek Ostaszewski avatar Marek OstaszewskiXavier Garnier avatar Xavier GarnierDaniel Maticzka avatar Daniel MaticzkaBelinda Phipson avatar Belinda Phipsonorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMira Kuntz avatar Mira KuntzJovana Maksimovic avatar Jovana MaksimovicSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamCharity Law avatar Charity Laworcid logoErwan Corre avatar Erwan Correorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

Funders

This material was funded by:

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

References