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:

orcid logoFlorian Heyl avatar Florian Heylorcid logoPavankumar Videm avatar Pavankumar VidemSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamOlivier Dameron avatar Olivier DameronMatt Ritchie avatar Matt Ritchieorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzMehmet Tekman avatar Mehmet Tekmanorcid logoClea Siguret avatar Clea Siguretorcid logoClemens Blank avatar Clemens BlankAnna Trigos avatar Anna Trigosorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoHelena Rasche avatar Helena RascheAnton Nekrutenko avatar Anton NekrutenkoJames Taylor avatar James TaylorNiall Beard avatar Niall BeardMarius van den Beek avatar Marius van den Beekorcid logoSaskia Hiltemann avatar Saskia HiltemannBelinda Phipson avatar Belinda PhipsonAndrea Bagnacani avatar Andrea Bagnacaniorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoBjörn Grüning avatar Björn Grüningorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMaria Doyle avatar Maria DoyleXavier Garnier avatar Xavier GarnierXi Liu avatar Xi Liuorcid logoErwan Corre avatar Erwan Correorcid logoPeter van Heusden avatar Peter van HeusdenWilliam Durand avatar William Durandorcid logoMo Heydarian avatar Mo Heydarianorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiJovana Maksimovic avatar Jovana MaksimovicSimon Bray avatar Simon Brayorcid logoMateo Boudet avatar Mateo BoudetCharity Law avatar Charity Laworcid logoLinelle Abueg avatar Linelle Abuegorcid logoTeresa Müller avatar Teresa Müllerorcid logoAnne Fouilloux avatar Anne FouillouxJosé Manuel Domínguez avatar José Manuel DomínguezDaniel Maticzka avatar Daniel Maticzkaorcid logoMira Kuntz avatar Mira Kuntzorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoNicola Soranzo avatar Nicola SoranzoAnne Siegel avatar Anne Siegelorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoBérénice Batut avatar Bérénice Batutorcid logoMatti Hoch avatar Matti HochMateusz Kuzak avatar Mateusz KuzakHarriet Dashnow avatar Harriet Dashnoworcid logoArmin Dadras avatar Armin Dadrasorcid logoGraeme Tyson avatar Graeme Tysonorcid logoLucille Delisle avatar Lucille Delisleorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMartin Čech avatar Martin ČechShian Su avatar Shian Suorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkEkaterina Polkh avatar Ekaterina Polkhorcid logoToby Hodges avatar Toby HodgesIGC Bioinformatics Unit avatar IGC Bioinformatics UnitGildas Le Corguillé avatar Gildas Le CorguilléMarkus Wolfien avatar Markus WolfienChao Zhang avatar Chao Zhang

Funding

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

References