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 logoMira Kuntz avatar Mira Kuntzorcid logoMo Heydarian avatar Mo HeydarianMarkus Wolfien avatar Markus WolfienIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoLucille Delisle avatar Lucille DelisleJosé Manuel Domínguez avatar José Manuel DomínguezMehmet Tekman avatar Mehmet Tekmanorcid logoAnika Erxleben avatar Anika ErxlebenHarriet Dashnow avatar Harriet DashnowBelinda Phipson avatar Belinda PhipsonAnna Trigos avatar Anna Trigosorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiDaniel Maticzka avatar Daniel Maticzkaorcid logoBjörn Grüning avatar Björn GrüningXavier Garnier avatar Xavier Garnierorcid logoToby Hodges avatar Toby Hodgesorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoFlorian Heyl avatar Florian HeylAnne Siegel avatar Anne Siegelorcid logoMatti Hoch avatar Matti HochJovana Maksimovic avatar Jovana Maksimovicorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoNicola Soranzo avatar Nicola SoranzoSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamNiall Beard avatar Niall Beardorcid logoTeresa Müller avatar Teresa Müllerorcid logoMateo Boudet avatar Mateo Boudetorcid logoPavankumar Videm avatar Pavankumar VidemMarius van den Beek avatar Marius van den Beekorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoClea Siguret avatar Clea SiguretAndrea Bagnacani avatar Andrea Bagnacaniorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoBérénice Batut avatar Bérénice BatutChao Zhang avatar Chao ZhangCharity Law avatar Charity Laworcid logoMaria Doyle avatar Maria Doyleorcid logoMartin Čech avatar Martin Čechorcid logoErwan Corre avatar Erwan CorreMateusz Kuzak avatar Mateusz Kuzakorcid logoHelena Rasche avatar Helena Rascheorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMarek Ostaszewski avatar Marek OstaszewskiWilliam Durand avatar William Durandorcid logoArmin Dadras avatar Armin DadrasMatt Ritchie avatar Matt RitchieGildas Le Corguillé avatar Gildas Le CorguilléEkaterina Polkh avatar Ekaterina Polkhorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoJames Taylor avatar James Taylororcid logoLinelle Abueg avatar Linelle AbuegSimon Bray avatar Simon Brayorcid logoGraeme Tyson avatar Graeme Tysonorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoSaskia Hiltemann avatar Saskia HiltemannShian Su avatar Shian SuXi Liu avatar Xi Liuorcid logoClemens Blank avatar Clemens BlankOlivier Dameron avatar Olivier DameronAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoIacopo Cristoferi avatar Iacopo Cristoferi

Funding

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

References