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 logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoToby Hodges avatar Toby Hodgesorcid logoAnika Erxleben avatar Anika ErxlebenNiall Beard avatar Niall BeardGildas Le Corguillé avatar Gildas Le Corguilléorcid logoHelena Rasche avatar Helena RaschePeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoArmin Dadras avatar Armin Dadrasorcid logoMartin Čech avatar Martin ČechMehmet Tekman avatar Mehmet Tekmanorcid logoMateo Boudet avatar Mateo BoudetJovana Maksimovic avatar Jovana MaksimovicEkaterina Polkh avatar Ekaterina PolkhAnne Siegel avatar Anne SiegelSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoMaria Doyle avatar Maria Doyleorcid logoLucille Delisle avatar Lucille DelisleMateusz Kuzak avatar Mateusz KuzakAndrea Bagnacani avatar Andrea BagnacaniBelinda Phipson avatar Belinda PhipsonSimon Bray avatar Simon BrayCharlotte Adang avatar Charlotte Adangorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoTeresa Müller avatar Teresa Müllerorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoMira Kuntz avatar Mira Kuntzorcid logoMatti Hoch avatar Matti HochDaniel Maticzka avatar Daniel Maticzkaorcid logoClea Siguret avatar Clea SiguretOlivier Dameron avatar Olivier Dameronorcid logoMallory Freeberg avatar Mallory Freebergorcid logoSofoklis Keisaris avatar Sofoklis KeisarisMatt Ritchie avatar Matt RitchieJames Taylor avatar James Taylororcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoErwan Corre avatar Erwan Correorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoChao Zhang avatar Chao ZhangJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoFlorian Heyl avatar Florian HeylCasper de Visser avatar Casper de Visserorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoMo Heydarian avatar Mo Heydarianorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoCristóbal Gallardo avatar Cristóbal GallardoShian Su avatar Shian SuAnna Trigos avatar Anna TrigosXavier Garnier avatar Xavier GarnierCharity Law avatar Charity LawIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoLinelle Abueg avatar Linelle Abuegorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoBérénice Batut avatar Bérénice BatutHarriet Dashnow avatar Harriet DashnowXi Liu avatar Xi LiuMarkus Wolfien avatar Markus Wolfienorcid logoClemens Blank avatar Clemens BlankAnton Nekrutenko avatar Anton Nekrutenkoorcid logoGraeme Tyson avatar Graeme Tysonorcid logoPavankumar Videm avatar Pavankumar VidemWilliam Durand avatar William DurandMarius van den Beek avatar Marius van den Beekorcid logoBjörn Grüning avatar Björn Grüningorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

Funding

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

References