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:

Chao Zhang avatar Chao Zhangorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoClea Siguret avatar Clea SiguretCharlotte Adang avatar Charlotte Adangorcid logoClemens Blank avatar Clemens BlankBelinda Phipson avatar Belinda PhipsonEkaterina Polkh avatar Ekaterina PolkhSimon Bray avatar Simon BrayShian Su avatar Shian SuCasper de Visser avatar Casper de Visserorcid logoHelena Rasche avatar Helena Rascheorcid logoGraeme Tyson avatar Graeme TysonMateusz Kuzak avatar Mateusz KuzakMarius van den Beek avatar Marius van den BeekWilliam Durand avatar William DurandAndrea Bagnacani avatar Andrea BagnacaniJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoToby Hodges avatar Toby HodgesOlivier Dameron avatar Olivier DameronIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoArmin Dadras avatar Armin Dadrasorcid logoErwan Corre avatar Erwan CorreXavier Garnier avatar Xavier GarnierDaniel Maticzka avatar Daniel Maticzkaorcid logoBérénice Batut avatar Bérénice BatutJames Taylor avatar James TaylorGildas Le Corguillé avatar Gildas Le CorguilléMehmet Tekman avatar Mehmet Tekmanorcid logoMartin Čech avatar Martin Čechorcid logoMo Heydarian avatar Mo HeydarianAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMateo Boudet avatar Mateo Boudetorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMaria Doyle avatar Maria DoylePeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoAnika Erxleben avatar Anika ErxlebenHarriet Dashnow avatar Harriet Dashnoworcid logoFlorian Heyl avatar Florian Heylorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoMira Kuntz avatar Mira KuntzAnna Trigos avatar Anna Trigosorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoMatti Hoch avatar Matti Hochorcid logoBjörn Grüning avatar Björn GrüningCharity Law avatar Charity LawMarkus Wolfien avatar Markus WolfienAnne Siegel avatar Anne SiegelSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAnne Fouilloux avatar Anne FouillouxMatt Ritchie avatar Matt Ritchieorcid logoLinelle Abueg avatar Linelle Abuegorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoMallory Freeberg avatar Mallory Freebergorcid logoLucille Delisle avatar Lucille Delisleorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoTeresa Müller avatar Teresa Müllerorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosNiall Beard avatar Niall Beardorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoAnthony Bretaudeau avatar Anthony BretaudeauJovana Maksimovic avatar Jovana Maksimovicorcid logoPavankumar Videm avatar Pavankumar VidemXi Liu avatar Xi Liuorcid logoNicola Soranzo avatar Nicola Soranzo

Funding

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

References