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 logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoFlorian Heyl avatar Florian Heylorcid logoLucille Delisle avatar Lucille DelisleIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoAnika Erxleben avatar Anika ErxlebenBelinda Phipson avatar Belinda PhipsonEkaterina Polkh avatar Ekaterina Polkhorcid logoPeter van Heusden avatar Peter van HeusdenDaniel Maticzka avatar Daniel MaticzkaAnna Trigos avatar Anna TrigosSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoMo Heydarian avatar Mo Heydarianorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosGildas Le Corguillé avatar Gildas Le CorguilléChao Zhang avatar Chao Zhangorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoToby Hodges avatar Toby Hodgesorcid logoMartin Čech avatar Martin Čechorcid logoLinelle Abueg avatar Linelle Abuegorcid logoBérénice Batut avatar Bérénice BatutMateusz Kuzak avatar Mateusz KuzakAnne Siegel avatar Anne SiegelAnton Nekrutenko avatar Anton Nekrutenkoorcid logoClea Siguret avatar Clea Siguretorcid logoClemens Blank avatar Clemens BlankCharity Law avatar Charity Laworcid logoNicola Soranzo avatar Nicola SoranzoMatt Ritchie avatar Matt Ritchieorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAnthony Bretaudeau avatar Anthony BretaudeauHarriet Dashnow avatar Harriet Dashnoworcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiXavier Garnier avatar Xavier Garnierorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoBjörn Grüning avatar Björn GrüningAndrea Bagnacani avatar Andrea Bagnacaniorcid logoGraeme Tyson avatar Graeme Tysonorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoWolfgang Maier avatar Wolfgang MaierMehmet Tekman avatar Mehmet Tekmanorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoHelena Rasche avatar Helena Rascheorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoMateo Boudet avatar Mateo BoudetMarius van den Beek avatar Marius van den BeekMarkus Wolfien avatar Markus WolfienNiall Beard avatar Niall BeardJovana Maksimovic avatar Jovana Maksimovicorcid logoMira Kuntz avatar Mira KuntzSimon Bray avatar Simon BrayJosé Manuel Domínguez avatar José Manuel DomínguezOlivier Dameron avatar Olivier DameronWilliam Durand avatar William DurandJames Taylor avatar James Taylororcid logoMatti Hoch avatar Matti HochXi Liu avatar Xi Liuorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoMaria Doyle avatar Maria Doyleorcid logoErwan Corre avatar Erwan CorreShian Su avatar Shian Su

Funding

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

References