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.

Follow topic updates rss-feed with our RSS Feed

Community Resources

Community Home Maintainer Home

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:

Olivier Dameron avatar Olivier DameronGildas Le Corguillé avatar Gildas Le CorguilléDaniel Maticzka avatar Daniel MaticzkaShian Su avatar Shian SuSimon Bray avatar Simon BrayBelinda Phipson avatar Belinda PhipsonMateusz Kuzak avatar Mateusz Kuzakorcid logoMira Kuntz avatar Mira KuntzMatt Ritchie avatar Matt Ritchieorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoErwan Corre avatar Erwan Correorcid logoClea Siguret avatar Clea Siguretorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoLucille Delisle avatar Lucille DelisleMehmet Tekman avatar Mehmet Tekmanorcid logoBjörn Grüning avatar Björn Grüningorcid logoMo Heydarian avatar Mo Heydarianorcid logoAnthony Bretaudeau avatar Anthony BretaudeauHarriet Dashnow avatar Harriet DashnowAnna Trigos avatar Anna TrigosMarkus Wolfien avatar Markus WolfienWilliam Durand avatar William Durandorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoCristóbal Gallardo avatar Cristóbal GallardoJovana Maksimovic avatar Jovana MaksimovicJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoGraeme Tyson avatar Graeme TysonSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamAndrea Bagnacani avatar Andrea Bagnacaniorcid logoFlorian Heyl avatar Florian HeylNiall Beard avatar Niall Beardorcid logoMallory Freeberg avatar Mallory Freebergorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoWolfgang Maier avatar Wolfgang MaierChao Zhang avatar Chao Zhangorcid logoClemens Blank avatar Clemens Blankorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzCasper de Visser avatar Casper de Visserorcid logoMaria Doyle avatar Maria DoyleXi Liu avatar Xi Liuorcid logoLinelle Abueg avatar Linelle AbuegPeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoToby Hodges avatar Toby HodgesMarius van den Beek avatar Marius van den Beekorcid logoMateo Boudet avatar Mateo BoudetCharlotte Adang avatar Charlotte Adangorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnne Fouilloux avatar Anne FouillouxJames Taylor avatar James TaylorAnton Nekrutenko avatar Anton NekrutenkoEkaterina Polkh avatar Ekaterina PolkhAnne Siegel avatar Anne SiegelCharity Law avatar Charity Laworcid logoArmin Dadras avatar Armin DadrasXavier Garnier avatar Xavier GarnierIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoHelena Rasche avatar Helena Rascheorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoTeresa Müller avatar Teresa Müllerorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoMatti Hoch avatar Matti Hochorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoMartin Čech avatar Martin Čech

Funding

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

References