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

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Contributors

This material was contributed to by:

Belinda Phipson avatar Belinda Phipsonorcid logoLucille Delisle avatar Lucille DelisleXi Liu avatar Xi LiuMarius van den Beek avatar Marius van den Beekorcid logoToby Hodges avatar Toby HodgesWilliam Durand avatar William DurandShian Su avatar Shian Suorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoMateo Boudet avatar Mateo Boudetorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoHelena Rasche avatar Helena Rascheorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoClea Siguret avatar Clea Siguretorcid logoMaria Doyle avatar Maria Doyleorcid logoTeresa Müller avatar Teresa Müllerorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkJames Taylor avatar James TaylorXavier Garnier avatar Xavier Garnierorcid logoArmin Dadras avatar Armin DadrasMehmet Tekman avatar Mehmet Tekmanorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoBérénice Batut avatar Bérénice Batutorcid logoErwan Corre avatar Erwan Correorcid logoMartin Čech avatar Martin Čechorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoWolfgang Maier avatar Wolfgang MaierCasper de Visser avatar Casper de VisserIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoGraeme Tyson avatar Graeme TysonNiall Beard avatar Niall BeardCharlotte Adang avatar Charlotte Adangorcid logoMallory Freeberg avatar Mallory FreebergOlivier Dameron avatar Olivier Dameronorcid logoMatti Hoch avatar Matti HochAnton Nekrutenko avatar Anton Nekrutenkoorcid logoFlorian Heyl avatar Florian HeylMatt Ritchie avatar Matt Ritchieorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoMarkus Wolfien avatar Markus Wolfienorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoSofoklis Keisaris avatar Sofoklis KeisarisHarriet Dashnow avatar Harriet DashnowSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamAnne Siegel avatar Anne SiegelJovana Maksimovic avatar Jovana Maksimovicorcid logoMira Kuntz avatar Mira Kuntzorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosJosé Manuel Domínguez avatar José Manuel DomínguezPeter-Bram 't Hoen avatar Peter-Bram 't HoenAnna Trigos avatar Anna Trigosorcid logoLinelle Abueg avatar Linelle Abuegorcid logoClemens Blank avatar Clemens BlankChao Zhang avatar Chao Zhangorcid logoSaskia Hiltemann avatar Saskia HiltemannSimon Bray avatar Simon BrayAndrea Bagnacani avatar Andrea Bagnacaniorcid logoCristóbal Gallardo avatar Cristóbal GallardoGildas Le Corguillé avatar Gildas Le Corguilléorcid logoBjörn Grüning avatar Björn Grüningorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzEkaterina Polkh avatar Ekaterina Polkhorcid logoNicola Soranzo avatar Nicola SoranzoMateusz Kuzak avatar Mateusz Kuzakorcid logoMo Heydarian avatar Mo HeydarianDaniel Maticzka avatar Daniel MaticzkaCharity Law avatar Charity Law

Funding

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

References