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 logoSaskia Hiltemann avatar Saskia HiltemannCharlotte Adang avatar Charlotte AdangEkaterina Polkh avatar Ekaterina Polkhorcid logoClea Siguret avatar Clea Siguretorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoGraeme Tyson avatar Graeme TysonChao Zhang avatar Chao Zhangorcid logoBérénice Batut avatar Bérénice Batutorcid logoTeresa Müller avatar Teresa Müllerorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMaria Doyle avatar Maria DoyleJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoCristóbal Gallardo avatar Cristóbal GallardoOlivier Dameron avatar Olivier DameronSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoLinelle Abueg avatar Linelle Abuegorcid logoMo Heydarian avatar Mo HeydarianNiall Beard avatar Niall Beardorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoLucille Delisle avatar Lucille Delisleorcid logoFlorian Heyl avatar Florian HeylSimon Bray avatar Simon Brayorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoWolfgang Maier avatar Wolfgang MaierCharity Law avatar Charity LawAnna Trigos avatar Anna TrigosHarriet Dashnow avatar Harriet DashnowCasper de Visser avatar Casper de Visserorcid logoHelena Rasche avatar Helena RascheXavier Garnier avatar Xavier Garnierorcid logoMarek Ostaszewski avatar Marek OstaszewskiMateusz Kuzak avatar Mateusz Kuzakorcid logoBjörn Grüning avatar Björn GrüningMatt Ritchie avatar Matt RitchieJovana Maksimovic avatar Jovana Maksimovicorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoArmin Dadras avatar Armin Dadrasorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkDaniel Maticzka avatar Daniel Maticzkaorcid logoClemens Blank avatar Clemens BlankMarkus Wolfien avatar Markus Wolfienorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMira Kuntz avatar Mira Kuntzorcid logoErwan Corre avatar Erwan Correorcid logoMateo Boudet avatar Mateo Boudetorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiAndrea Bagnacani avatar Andrea Bagnacaniorcid logoPeter van Heusden avatar Peter van HeusdenJames Taylor avatar James TaylorXi Liu avatar Xi Liuorcid logoMartin Čech avatar Martin Čechorcid logoIacopo Cristoferi avatar Iacopo CristoferiMarius van den Beek avatar Marius van den BeekBelinda Phipson avatar Belinda Phipsonorcid logoToby Hodges avatar Toby HodgesIGC Bioinformatics Unit avatar IGC Bioinformatics UnitMehmet Tekman avatar Mehmet TekmanPeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoMallory Freeberg avatar Mallory FreebergShian Su avatar Shian SuWilliam Durand avatar William Durandorcid logoMatti Hoch avatar Matti HochGildas Le Corguillé avatar Gildas Le CorguilléAnne Siegel avatar Anne Siegelorcid logoPavankumar Videm avatar Pavankumar Videm

Funding

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

References