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:

Belinda Phipson avatar Belinda PhipsonGildas Le Corguillé avatar Gildas Le Corguilléorcid logoToby Hodges avatar Toby HodgesDaniel Maticzka avatar Daniel MaticzkaSimon Bray avatar Simon BrayMarkus Wolfien avatar Markus WolfienMateusz Kuzak avatar Mateusz Kuzakorcid logoMartin Čech avatar Martin Čechorcid logoHelena Rasche avatar Helena RascheWilliam Durand avatar William Durandorcid logoWolfgang Maier avatar Wolfgang MaierShian Su avatar Shian SuMehmet Tekman avatar Mehmet TekmanJames Taylor avatar James TaylorSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiAnne Siegel avatar Anne Siegelorcid logoErwan Corre avatar Erwan Correorcid logoCristóbal Gallardo avatar Cristóbal GallardoAndrea Bagnacani avatar Andrea Bagnacaniorcid logoLucille Delisle avatar Lucille Delisleorcid logoMateo Boudet avatar Mateo Boudetorcid logoLinelle Abueg avatar Linelle AbuegAnna Trigos avatar Anna Trigosorcid logoPeter van Heusden avatar Peter van HeusdenEkaterina Polkh avatar Ekaterina Polkhorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzChao Zhang avatar Chao Zhangorcid logoClemens Blank avatar Clemens BlankMatt Ritchie avatar Matt Ritchieorcid logoClea Siguret avatar Clea SiguretAnton Nekrutenko avatar Anton NekrutenkoJovana Maksimovic avatar Jovana Maksimovicorcid logoFlorian Heyl avatar Florian Heylorcid logoBjörn Grüning avatar Björn GrüningOlivier Dameron avatar Olivier Dameronorcid logoMo Heydarian avatar Mo HeydarianJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMatti Hoch avatar Matti Hochorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoMaria Doyle avatar Maria Doyleorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkHarriet Dashnow avatar Harriet Dashnoworcid logoSaskia Hiltemann avatar Saskia HiltemannCharity Law avatar Charity Laworcid logoPavankumar Videm avatar Pavankumar VidemMarius van den Beek avatar Marius van den BeekXi Liu avatar Xi Liuorcid logoMira Kuntz avatar Mira Kuntzorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoNicola Soranzo avatar Nicola SoranzoNiall Beard avatar Niall BeardIGC Bioinformatics Unit avatar IGC Bioinformatics UnitXavier Garnier avatar Xavier Garnierorcid logoGraeme Tyson avatar Graeme Tyson

Funding

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

References