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

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Contributors

This material was contributed to by:

Jovana Maksimovic avatar Jovana MaksimovicChao Zhang avatar Chao ZhangGildas Le Corguillé avatar Gildas Le Corguilléorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoLinelle Abueg avatar Linelle AbuegAnna Trigos avatar Anna TrigosAndrea Bagnacani avatar Andrea Bagnacaniorcid logoClemens Blank avatar Clemens BlankMarkus Wolfien avatar Markus WolfienIGC Bioinformatics Unit avatar IGC Bioinformatics UnitXi Liu avatar Xi LiuCharity Law avatar Charity Laworcid logoSofoklis Keisaris avatar Sofoklis KeisarisSimon Bray avatar Simon Brayorcid logoMallory Freeberg avatar Mallory Freebergorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiAnton Nekrutenko avatar Anton Nekrutenkoorcid logoPeter van Heusden avatar Peter van HeusdenHarriet Dashnow avatar Harriet Dashnoworcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosWilliam Durand avatar William Durandorcid logoMateo Boudet avatar Mateo Boudetorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoMatti Hoch avatar Matti Hochorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoMartin Čech avatar Martin Čechorcid logoGraeme Tyson avatar Graeme Tysonorcid logoTeresa Müller avatar Teresa Müllerorcid logoMaria Doyle avatar Maria DoyleMateusz Kuzak avatar Mateusz KuzakSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoArmin Dadras avatar Armin Dadrasorcid logoClea Siguret avatar Clea SiguretXavier Garnier avatar Xavier Garnierorcid logoFlorian Heyl avatar Florian HeylMatt Ritchie avatar Matt Ritchieorcid logoBjörn Grüning avatar Björn GrüningJames Taylor avatar James Taylororcid logoMo Heydarian avatar Mo Heydarianorcid logoAnthony Bretaudeau avatar Anthony BretaudeauShian Su avatar Shian Suorcid logoMira Kuntz avatar Mira Kuntzorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoHelena Rasche avatar Helena RascheBelinda Phipson avatar Belinda Phipsonorcid logoAnne Fouilloux avatar Anne FouillouxEkaterina Polkh avatar Ekaterina PolkhOlivier Dameron avatar Olivier DameronDaniel Maticzka avatar Daniel Maticzkaorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoNiall Beard avatar Niall Beardorcid logoErwan Corre avatar Erwan Correorcid logoSaskia Hiltemann avatar Saskia HiltemannCasper de Visser avatar Casper de Visserorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBérénice Batut avatar Bérénice BatutMarius van den Beek avatar Marius van den BeekCharlotte Adang avatar Charlotte Adangorcid logoLucille Delisle avatar Lucille Delisleorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoWolfgang Maier avatar Wolfgang MaierMehmet Tekman avatar Mehmet Tekmanorcid logoToby Hodges avatar Toby HodgesAnne Siegel avatar Anne SiegelPeter-Bram 't Hoen avatar Peter-Bram 't HoenJosé Manuel Domínguez avatar José Manuel Domínguez

Funding

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

References