Transcriptomics

Training material for all kinds of transcriptomics analysis.

Requirements

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

Material

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

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

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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Community Resources

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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

Contributors

This material was contributed to by:

Simon Bray avatar Simon BrayMarius van den Beek avatar Marius van den BeekMarkus Wolfien avatar Markus Wolfienorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoSofoklis Keisaris avatar Sofoklis KeisarisJames Taylor avatar James Taylororcid logoMallory Freeberg avatar Mallory FreebergAndrea Bagnacani avatar Andrea BagnacaniAnne Siegel avatar Anne SiegelMatt Ritchie avatar Matt RitchieOlivier Dameron avatar Olivier DameronXi Liu avatar Xi LiuBelinda Phipson avatar Belinda Phipsonorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoGraeme Tyson avatar Graeme Tysonorcid logoMateo Boudet avatar Mateo BoudetShian Su avatar Shian Suorcid logoBérénice Batut avatar Bérénice Batutorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoMira Kuntz avatar Mira Kuntzorcid logoMaria Doyle avatar Maria Doyleorcid logoMartin Čech avatar Martin Čechorcid logoToby Hodges avatar Toby HodgesJovana Maksimovic avatar Jovana MaksimovicDaniel Maticzka avatar Daniel MaticzkaAnna Trigos avatar Anna Trigosorcid logoAnne Fouilloux avatar Anne FouillouxWilliam Durand avatar William Durandorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoWolfgang Maier avatar Wolfgang MaierMateusz Kuzak avatar Mateusz Kuzakorcid logoBjörn Grüning avatar Björn GrüningJosé Manuel Domínguez avatar José Manuel DomínguezSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoHelena Rasche avatar Helena Rascheorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoErwan Corre avatar Erwan CorreGildas Le Corguillé avatar Gildas Le CorguilléAnton Nekrutenko avatar Anton NekrutenkoXavier Garnier avatar Xavier GarnierCharity Law avatar Charity Laworcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkNiall Beard avatar Niall Beardorcid logoFlorian Heyl avatar Florian HeylIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoMatti Hoch avatar Matti HochEkaterina Polkh avatar Ekaterina Polkhorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoClea Siguret avatar Clea Siguretorcid logoClemens Blank avatar Clemens Blankorcid logoSaskia Hiltemann avatar Saskia HiltemannMehmet Tekman avatar Mehmet Tekmanorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoLucille Delisle avatar Lucille Delisleorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoCristóbal Gallardo avatar Cristóbal GallardoHarriet Dashnow avatar Harriet Dashnoworcid logoMo Heydarian avatar Mo Heydarianorcid logoLinelle Abueg avatar Linelle AbuegChao Zhang avatar Chao Zhang

Funding

These individuals or organisations provided funding support for the development of this resource

References