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

Are you on the editorial board or want to help out with this topic? View the topic maintainer page for ways to improve this topic!

Contributors

This material was contributed to by:

orcid logoAnne Fouilloux avatar Anne FouillouxMatt Ritchie avatar Matt Ritchieorcid logoErwan Corre avatar Erwan Correorcid logoMaria Doyle avatar Maria Doyleorcid logoBérénice Batut avatar Bérénice BatutAnna Trigos avatar Anna TrigosJames Taylor avatar James TaylorEkaterina Polkh avatar Ekaterina Polkhorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoClemens Blank avatar Clemens BlankChao Zhang avatar Chao ZhangOlivier Dameron avatar Olivier DameronXi Liu avatar Xi Liuorcid logoPavankumar Videm avatar Pavankumar VidemSimon Bray avatar Simon Brayorcid logoMatti Hoch avatar Matti Hochorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoGraeme Tyson avatar Graeme TysonAndrea Bagnacani avatar Andrea Bagnacaniorcid logoBjörn Grüning avatar Björn Grüningorcid logoMartin Čech avatar Martin Čechorcid logoPeter van Heusden avatar Peter van HeusdenBelinda Phipson avatar Belinda Phipsonorcid logoArmin Dadras avatar Armin DadrasCasper de Visser avatar Casper de Visserorcid logoCristóbal Gallardo avatar Cristóbal GallardoNiall Beard avatar Niall Beardorcid logoIacopo Cristoferi avatar Iacopo CristoferiJovana Maksimovic avatar Jovana Maksimovicorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoSaskia Hiltemann avatar Saskia HiltemannHarriet Dashnow avatar Harriet Dashnoworcid logoMateo Boudet avatar Mateo BoudetSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamMehmet Tekman avatar Mehmet TekmanMarius van den Beek avatar Marius van den Beekorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoLucille Delisle avatar Lucille DelisleXavier Garnier avatar Xavier Garnierorcid logoHelena Rasche avatar Helena RaschePeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoMo Heydarian avatar Mo Heydarianorcid logoToby Hodges avatar Toby Hodgesorcid logoMarek Ostaszewski avatar Marek OstaszewskiAnne Siegel avatar Anne Siegelorcid logoMira Kuntz avatar Mira KuntzCharity Law avatar Charity LawWilliam Durand avatar William Durandorcid logoFlorian Heyl avatar Florian Heylorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoClea Siguret avatar Clea Siguretorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkMateusz Kuzak avatar Mateusz Kuzakorcid logoLinelle Abueg avatar Linelle AbuegIGC Bioinformatics Unit avatar IGC Bioinformatics UnitCharlotte Adang avatar Charlotte AdangDaniel Maticzka avatar Daniel MaticzkaAnton Nekrutenko avatar Anton NekrutenkoMarkus Wolfien avatar Markus Wolfienorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoTeresa Müller avatar Teresa MüllerJosé Manuel Domínguez avatar José Manuel DomínguezGildas Le Corguillé avatar Gildas Le Corguilléorcid logoMallory Freeberg avatar Mallory Freebergorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoShian Su avatar Shian Su

Funding

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

References