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 logoAnthony Bretaudeau avatar Anthony BretaudeauDaniel Maticzka avatar Daniel Maticzkaorcid logoAnne Fouilloux avatar Anne FouillouxEkaterina Polkh avatar Ekaterina Polkhorcid logoGraeme Tyson avatar Graeme Tysonorcid logoHelena Rasche avatar Helena Rascheorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoMallory Freeberg avatar Mallory FreebergMatt Ritchie avatar Matt RitchieXi Liu avatar Xi LiuPeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoFlorian Heyl avatar Florian Heylorcid logoAnika Erxleben avatar Anika ErxlebenAnton Nekrutenko avatar Anton NekrutenkoJovana Maksimovic avatar Jovana Maksimovicorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoErwan Corre avatar Erwan Correorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosCharlotte Adang avatar Charlotte Adangorcid logoArmin Dadras avatar Armin DadrasCasper de Visser avatar Casper de VisserWilliam Durand avatar William Durandorcid logoNicola Soranzo avatar Nicola SoranzoBelinda Phipson avatar Belinda PhipsonGildas Le Corguillé avatar Gildas Le Corguilléorcid logoMaria Doyle avatar Maria Doyleorcid logoBérénice Batut avatar Bérénice Batutorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoMo Heydarian avatar Mo HeydarianChao Zhang avatar Chao Zhangorcid logoTeresa Müller avatar Teresa MüllerIGC Bioinformatics Unit avatar IGC Bioinformatics UnitOlivier Dameron avatar Olivier DameronJames Taylor avatar James Taylororcid logoMira Kuntz avatar Mira Kuntzorcid logoPavankumar Videm avatar Pavankumar VidemJosé Manuel Domínguez avatar José Manuel DomínguezXavier Garnier avatar Xavier Garnierorcid logoClemens Blank avatar Clemens BlankMateusz Kuzak avatar Mateusz KuzakHarriet Dashnow avatar Harriet Dashnoworcid logoMateo Boudet avatar Mateo BoudetAnna Trigos avatar Anna Trigosorcid logoIacopo Cristoferi avatar Iacopo CristoferiMehmet Tekman avatar Mehmet TekmanSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamSimon Bray avatar Simon Brayorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoToby Hodges avatar Toby Hodgesorcid logoLucille Delisle avatar Lucille DelisleMarius van den Beek avatar Marius van den BeekShian Su avatar Shian SuCharity Law avatar Charity Laworcid logoSofoklis Keisaris avatar Sofoklis KeisarisAndrea Bagnacani avatar Andrea Bagnacaniorcid logoMatti Hoch avatar Matti HochAnne Siegel avatar Anne Siegelorcid logoLinelle Abueg avatar Linelle Abuegorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzNiall Beard avatar Niall Beardorcid logoBjörn Grüning avatar Björn Grüningorcid logoMartin Čech avatar Martin ČechMarkus Wolfien avatar Markus Wolfienorcid logoClea Siguret avatar Clea Siguretorcid logoPeter van Heusden avatar Peter van Heusden

Funding

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

References