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 logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoBjörn Grüning avatar Björn Grüningorcid logoErwan Corre avatar Erwan Correorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosAnton Nekrutenko avatar Anton NekrutenkoSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoNicola Soranzo avatar Nicola SoranzoGildas Le Corguillé avatar Gildas Le Corguilléorcid logoBérénice Batut avatar Bérénice Batutorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoAnika Erxleben avatar Anika ErxlebenChao Zhang avatar Chao ZhangMatt Ritchie avatar Matt Ritchieorcid logoMo Heydarian avatar Mo Heydarianorcid logoClemens Blank avatar Clemens Blankorcid logoMarek Ostaszewski avatar Marek OstaszewskiDaniel Maticzka avatar Daniel MaticzkaJames Taylor avatar James Taylororcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoMarkus Wolfien avatar Markus Wolfienorcid logoSaskia Hiltemann avatar Saskia HiltemannAndrea Bagnacani avatar Andrea BagnacaniCharity Law avatar Charity LawIGC Bioinformatics Unit avatar IGC Bioinformatics UnitOlivier Dameron avatar Olivier Dameronorcid logoHelena Rasche avatar Helena RascheAnne Siegel avatar Anne Siegelorcid logoPavankumar Videm avatar Pavankumar VidemThe Carpentries avatar The CarpentriesShian Su avatar Shian Suorcid logoToby Hodges avatar Toby HodgesJovana Maksimovic avatar Jovana MaksimovicAnna Trigos avatar Anna TrigosJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoMallory Freeberg avatar Mallory Freebergorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMateo Boudet avatar Mateo BoudetXi Liu avatar Xi Liuorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoFlorian Heyl avatar Florian Heylorcid logoMatti Hoch avatar Matti Hochorcid logoLucille Delisle avatar Lucille DelisleBelinda Phipson avatar Belinda PhipsonHarriet Dashnow avatar Harriet Dashnoworcid logoIacopo Cristoferi avatar Iacopo CristoferiXavier Garnier avatar Xavier Garnierorcid logoMaria Doyle avatar Maria Doyleorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoMira Kuntz avatar Mira Kuntz

Funders

This material was funded by:

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

References