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:

Charity Law avatar Charity LawMarius van den Beek avatar Marius van den BeekEkaterina Polkh avatar Ekaterina PolkhBelinda Phipson avatar Belinda PhipsonChao Zhang avatar Chao Zhangorcid logoBérénice Batut avatar Bérénice Batutorcid logoMo Heydarian avatar Mo HeydarianCasper de Visser avatar Casper de Visserorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoMartin Čech avatar Martin ČechJames Taylor avatar James Taylororcid logoClemens Blank avatar Clemens Blankorcid logoMaria Doyle avatar Maria DoyleNiall Beard avatar Niall Beardorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoBjörn Grüning avatar Björn GrüningXavier Garnier avatar Xavier GarnierWilliam Durand avatar William Durandorcid logoWolfgang Maier avatar Wolfgang MaierIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiOlivier Dameron avatar Olivier Dameronorcid logoAnika Erxleben avatar Anika ErxlebenAnne Siegel avatar Anne SiegelSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMira Kuntz avatar Mira KuntzHarriet Dashnow avatar Harriet Dashnoworcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoErwan Corre avatar Erwan CorreCharlotte Adang avatar Charlotte AdangGildas Le Corguillé avatar Gildas Le CorguilléAnna Trigos avatar Anna Trigosorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoAnthony Bretaudeau avatar Anthony BretaudeauMarkus Wolfien avatar Markus Wolfienorcid logoMallory Freeberg avatar Mallory FreebergShian Su avatar Shian SuAnton Nekrutenko avatar Anton NekrutenkoAndrea Bagnacani avatar Andrea Bagnacaniorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoHelena Rasche avatar Helena Rascheorcid logoLinelle Abueg avatar Linelle AbuegMatt Ritchie avatar Matt Ritchieorcid logoFlorian Heyl avatar Florian HeylJovana Maksimovic avatar Jovana MaksimovicJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoClea Siguret avatar Clea Siguretorcid logoLucille Delisle avatar Lucille Delisleorcid logoPavankumar Videm avatar Pavankumar VidemSimon Bray avatar Simon Brayorcid logoTeresa Müller avatar Teresa Müllerorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoGraeme Tyson avatar Graeme TysonMehmet Tekman avatar Mehmet TekmanPeter-Bram 't Hoen avatar Peter-Bram 't HoenDaniel Maticzka avatar Daniel Maticzkaorcid logoToby Hodges avatar Toby Hodgesorcid logoArmin Dadras avatar Armin Dadrasorcid logoMatti Hoch avatar Matti Hochorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoPeter van Heusden avatar Peter van HeusdenMateusz Kuzak avatar Mateusz KuzakXi Liu avatar Xi Liuorcid logoMateo Boudet avatar Mateo Boudet

Funding

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

References