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 logoLinelle Abueg avatar Linelle AbuegNiall Beard avatar Niall Beardorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoToby Hodges avatar Toby Hodgesorcid logoClea Siguret avatar Clea SiguretXi Liu avatar Xi Liuorcid logoAnne Fouilloux avatar Anne FouillouxMatt Ritchie avatar Matt RitchieWilliam Durand avatar William DurandCharity Law avatar Charity LawMehmet Tekman avatar Mehmet Tekmanorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoHelena Rasche avatar Helena Rascheorcid logoClemens Blank avatar Clemens BlankMarkus Wolfien avatar Markus WolfienAnne Siegel avatar Anne SiegelGildas Le Corguillé avatar Gildas Le CorguilléIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoMatti Hoch avatar Matti Hochorcid logoMarek Ostaszewski avatar Marek OstaszewskiAnna Trigos avatar Anna Trigosorcid logoMira Kuntz avatar Mira Kuntzorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoTeresa Müller avatar Teresa Müllerorcid logoBjörn Grüning avatar Björn GrüningSimon Bray avatar Simon Brayorcid logoMartin Čech avatar Martin ČechJames Taylor avatar James TaylorAndrea Bagnacani avatar Andrea Bagnacaniorcid logoErwan Corre avatar Erwan CorreHarriet Dashnow avatar Harriet Dashnoworcid logoAnika Erxleben avatar Anika Erxlebenorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoArmin Dadras avatar Armin DadrasMateusz Kuzak avatar Mateusz KuzakBelinda Phipson avatar Belinda Phipsonorcid logoFlorian Heyl avatar Florian Heylorcid logoGraeme Tyson avatar Graeme Tysonorcid logoPeter van Heusden avatar Peter van HeusdenAnton Nekrutenko avatar Anton Nekrutenkoorcid logoLucille Delisle avatar Lucille Delisleorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkShian Su avatar Shian SuSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoMallory Freeberg avatar Mallory FreebergMarius van den Beek avatar Marius van den Beekorcid logoBérénice Batut avatar Bérénice BatutJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMo Heydarian avatar Mo HeydarianEkaterina Polkh avatar Ekaterina Polkhorcid logoMaria Doyle avatar Maria Doyleorcid logoMateo Boudet avatar Mateo Boudetorcid logoWolfgang Maier avatar Wolfgang MaierJovana Maksimovic avatar Jovana MaksimovicDaniel Maticzka avatar Daniel MaticzkaOlivier Dameron avatar Olivier DameronChao Zhang avatar Chao ZhangXavier Garnier avatar Xavier Garnier

Funding

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

References