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

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 logoTeresa Müller avatar Teresa Müllerorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoLucille Delisle avatar Lucille DelisleJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoMaria Doyle avatar Maria DoyleMehmet Tekman avatar Mehmet Tekmanorcid logoMo Heydarian avatar Mo Heydarianorcid logoToby Hodges avatar Toby Hodgesorcid logoErwan Corre avatar Erwan CorreAndrea Bagnacani avatar Andrea Bagnacaniorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMatti Hoch avatar Matti HochOlivier Dameron avatar Olivier Dameronorcid logoArmin Dadras avatar Armin Dadrasorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosPeter-Bram 't Hoen avatar Peter-Bram 't HoenAnton Nekrutenko avatar Anton NekrutenkoAnna Trigos avatar Anna TrigosBelinda Phipson avatar Belinda Phipsonorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoBérénice Batut avatar Bérénice Batutorcid logoMartin Čech avatar Martin Čechorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoClea Siguret avatar Clea SiguretSimon Bray avatar Simon BrayAnne Siegel avatar Anne Siegelorcid logoBjörn Grüning avatar Björn GrüningJovana Maksimovic avatar Jovana Maksimovicorcid logoMira Kuntz avatar Mira Kuntzorcid logoGraeme Tyson avatar Graeme TysonXi Liu avatar Xi LiuShian Su avatar Shian Suorcid logoClemens Blank avatar Clemens BlankChao Zhang avatar Chao ZhangCharity Law avatar Charity LawDaniel Maticzka avatar Daniel Maticzkaorcid logoHelena Rasche avatar Helena Rascheorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoMateo Boudet avatar Mateo Boudetorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoNicola Soranzo avatar Nicola SoranzoSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamMateusz Kuzak avatar Mateusz Kuzakorcid logoLinelle Abueg avatar Linelle Abuegorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoNiall Beard avatar Niall BeardCasper de Visser avatar Casper de VisserIGC Bioinformatics Unit avatar IGC Bioinformatics UnitMatt Ritchie avatar Matt RitchieGildas Le Corguillé avatar Gildas Le Corguilléorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzMarius van den Beek avatar Marius van den BeekCharlotte Adang avatar Charlotte AdangWilliam Durand avatar William DurandJames Taylor avatar James Taylororcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkMarkus Wolfien avatar Markus WolfienXavier Garnier avatar Xavier GarnierEkaterina Polkh avatar Ekaterina PolkhHarriet Dashnow avatar Harriet Dashnoworcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoFlorian Heyl avatar Florian Heyl

Funding

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

References