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:

orcid logoMateo Boudet avatar Mateo BoudetMateusz Kuzak avatar Mateusz Kuzakorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoMartin Čech avatar Martin ČechAnton Nekrutenko avatar Anton NekrutenkoChao Zhang avatar Chao Zhangorcid logoBérénice Batut avatar Bérénice Batutorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoMatti Hoch avatar Matti HochMatt Ritchie avatar Matt RitchieAnna Trigos avatar Anna Trigosorcid logoWolfgang Maier avatar Wolfgang MaierXavier Garnier avatar Xavier GarnierHarriet Dashnow avatar Harriet DashnowGildas Le Corguillé avatar Gildas Le Corguilléorcid logoAnthony Bretaudeau avatar Anthony BretaudeauJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoMo Heydarian avatar Mo HeydarianDaniel Maticzka avatar Daniel MaticzkaSimon Bray avatar Simon Brayorcid logoHelena Rasche avatar Helena Rascheorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMira Kuntz avatar Mira Kuntzorcid logoMallory Freeberg avatar Mallory FreebergWilliam Durand avatar William DurandAnne Siegel avatar Anne SiegelNiall Beard avatar Niall BeardOlivier Dameron avatar Olivier DameronEkaterina Polkh avatar Ekaterina Polkhorcid logoArmin Dadras avatar Armin DadrasPeter-Bram 't Hoen avatar Peter-Bram 't HoenXi Liu avatar Xi LiuCasper de Visser avatar Casper de VisserCharlotte Adang avatar Charlotte Adangorcid logoFlorian Heyl avatar Florian Heylorcid logoTeresa Müller avatar Teresa Müllerorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoGraeme Tyson avatar Graeme Tysonorcid logoToby Hodges avatar Toby HodgesAndrea Bagnacani avatar Andrea Bagnacaniorcid logoClemens Blank avatar Clemens Blankorcid logoLinelle Abueg avatar Linelle Abuegorcid logoMaria Doyle avatar Maria DoyleMarkus Wolfien avatar Markus Wolfienorcid logoBjörn Grüning avatar Björn Grüningorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoCristóbal Gallardo avatar Cristóbal GallardoJovana Maksimovic avatar Jovana MaksimovicBelinda Phipson avatar Belinda Phipsonorcid logoPavankumar Videm avatar Pavankumar VidemSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamMarius van den Beek avatar Marius van den Beekorcid logoErwan Corre avatar Erwan Correorcid logoPeter van Heusden avatar Peter van HeusdenIGC Bioinformatics Unit avatar IGC Bioinformatics UnitJames Taylor avatar James Taylororcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoLucille Delisle avatar Lucille DelisleCharity Law avatar Charity LawShian Su avatar Shian Suorcid logoClea Siguret avatar Clea SiguretMehmet Tekman avatar Mehmet Tekmanorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoMarek Ostaszewski avatar Marek Ostaszewski

Funding

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

References