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:

orcid logoMarek Ostaszewski avatar Marek OstaszewskiJovana Maksimovic avatar Jovana Maksimovicorcid logoMo Heydarian avatar Mo HeydarianXavier Garnier avatar Xavier GarnierSimon Bray avatar Simon BrayXi Liu avatar Xi Liuorcid logoMateo Boudet avatar Mateo Boudetorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoMira Kuntz avatar Mira Kuntzorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoFlorian Heyl avatar Florian Heylorcid logoSofoklis Keisaris avatar Sofoklis KeisarisSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoPeter van Heusden avatar Peter van HeusdenShian Su avatar Shian SuDaniel Maticzka avatar Daniel Maticzkaorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoGraeme Tyson avatar Graeme Tysonorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoAnthony Bretaudeau avatar Anthony BretaudeauAnne Siegel avatar Anne Siegelorcid logoMatti Hoch avatar Matti Hochorcid logoClea Siguret avatar Clea Siguretorcid logoLinelle Abueg avatar Linelle AbuegMehmet Tekman avatar Mehmet Tekmanorcid logoMaria Doyle avatar Maria DoyleNiall Beard avatar Niall Beardorcid logoNicola Soranzo avatar Nicola SoranzoEkaterina Polkh avatar Ekaterina Polkhorcid logoMartin Čech avatar Martin Čechorcid logoHelena Rasche avatar Helena RascheWilliam Durand avatar William Durandorcid logoToby Hodges avatar Toby HodgesMateusz Kuzak avatar Mateusz Kuzakorcid logoCristóbal Gallardo avatar Cristóbal GallardoMatt Ritchie avatar Matt RitchieJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoBjörn Grüning avatar Björn Grüningorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzMarkus Wolfien avatar Markus WolfienCharity Law avatar Charity LawOlivier Dameron avatar Olivier Dameronorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoClemens Blank avatar Clemens Blankorcid logoAnika Erxleben avatar Anika ErxlebenMarius van den Beek avatar Marius van den Beekorcid logoBérénice Batut avatar Bérénice BatutBelinda Phipson avatar Belinda PhipsonAndrea Bagnacani avatar Andrea Bagnacaniorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosChao Zhang avatar Chao Zhangorcid logoLucille Delisle avatar Lucille DelisleAnna Trigos avatar Anna TrigosGildas Le Corguillé avatar Gildas Le CorguilléJames Taylor avatar James TaylorAnton Nekrutenko avatar Anton Nekrutenkoorcid logoErwan Corre avatar Erwan CorreIGC Bioinformatics Unit avatar IGC Bioinformatics UnitHarriet Dashnow avatar Harriet Dashnoworcid logoPavankumar Videm avatar Pavankumar Videmorcid logoMallory Freeberg avatar Mallory Freeberg

Funding

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

References