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 logoMatti Hoch avatar Matti HochJames Taylor avatar James TaylorChao Zhang avatar Chao Zhangorcid logoErwan Corre avatar Erwan CorreDaniel Maticzka avatar Daniel Maticzkaorcid logoClemens Blank avatar Clemens Blankorcid logoBjörn Grüning avatar Björn Grüningorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoBérénice Batut avatar Bérénice Batutorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoAnna Trigos avatar Anna TrigosJovana Maksimovic avatar Jovana Maksimovicorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMateo Boudet avatar Mateo BoudetOlivier Dameron avatar Olivier DameronAnne Siegel avatar Anne SiegelAndrea Bagnacani avatar Andrea BagnacaniIGC Bioinformatics Unit avatar IGC Bioinformatics UnitCharity Law avatar Charity Laworcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoToby Hodges avatar Toby Hodgesorcid logoMarek Ostaszewski avatar Marek OstaszewskiAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoLucille Delisle avatar Lucille DelisleMateusz Kuzak avatar Mateusz Kuzakorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoLinelle Abueg avatar Linelle AbuegMarius van den Beek avatar Marius van den BeekWilliam Durand avatar William DurandSimon Bray avatar Simon BrayGildas Le Corguillé avatar Gildas Le CorguilléMarkus Wolfien avatar Markus Wolfienorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoHelena Rasche avatar Helena Rascheorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoGraeme Tyson avatar Graeme Tysonorcid logoMaria Doyle avatar Maria Doyleorcid logoCristóbal Gallardo avatar Cristóbal GallardoShian Su avatar Shian Suorcid logoMartin Čech avatar Martin Čechorcid logoClea Siguret avatar Clea SiguretHarriet Dashnow avatar Harriet DashnowMehmet Tekman avatar Mehmet TekmanSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoSaskia Hiltemann avatar Saskia HiltemannJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoMo Heydarian avatar Mo HeydarianNiall Beard avatar Niall Beardorcid logoIacopo Cristoferi avatar Iacopo CristoferiEkaterina Polkh avatar Ekaterina Polkhorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMira Kuntz avatar Mira Kuntzorcid logoPavankumar Videm avatar Pavankumar VidemXavier Garnier avatar Xavier GarnierBelinda Phipson avatar Belinda PhipsonXi Liu avatar Xi LiuMatt Ritchie avatar Matt Ritchieorcid logoFlorian Heyl avatar Florian Heyl

Funding

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

References