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 logoMira Kuntz avatar Mira KuntzBelinda Phipson avatar Belinda PhipsonEkaterina Polkh avatar Ekaterina PolkhSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMateo Boudet avatar Mateo BoudetJovana Maksimovic avatar Jovana MaksimovicCharity Law avatar Charity Laworcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoAnne Fouilloux avatar Anne FouillouxAnna Trigos avatar Anna TrigosCharlotte Adang avatar Charlotte AdangXavier Garnier avatar Xavier Garnierorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoMo Heydarian avatar Mo Heydarianorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoTeresa Müller avatar Teresa MüllerOlivier Dameron avatar Olivier Dameronorcid logoMaria Doyle avatar Maria Doyleorcid logoClemens Blank avatar Clemens Blankorcid logoMallory Freeberg avatar Mallory FreebergIGC Bioinformatics Unit avatar IGC Bioinformatics UnitMarius van den Beek avatar Marius van den Beekorcid logoIacopo Cristoferi avatar Iacopo CristoferiCasper de Visser avatar Casper de Visserorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzHarriet Dashnow avatar Harriet DashnowJames Taylor avatar James TaylorNiall Beard avatar Niall BeardMehmet Tekman avatar Mehmet TekmanJosé Manuel Domínguez avatar José Manuel DomínguezAnne Siegel avatar Anne Siegelorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoMatti Hoch avatar Matti Hochorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiGildas Le Corguillé avatar Gildas Le Corguilléorcid logoLinelle Abueg avatar Linelle AbuegMatt Ritchie avatar Matt RitchieMateusz Kuzak avatar Mateusz KuzakSimon Bray avatar Simon Brayorcid logoFlorian Heyl avatar Florian Heylorcid logoClea Siguret avatar Clea Siguretorcid logoLucille Delisle avatar Lucille Delisleorcid logoErwan Corre avatar Erwan Correorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoGraeme Tyson avatar Graeme Tysonorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoToby Hodges avatar Toby HodgesShian Su avatar Shian Suorcid logoSaskia Hiltemann avatar Saskia HiltemannChao Zhang avatar Chao ZhangMarkus Wolfien avatar Markus WolfienWilliam Durand avatar William DurandDaniel Maticzka avatar Daniel Maticzkaorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoArmin Dadras avatar Armin DadrasAndrea Bagnacani avatar Andrea Bagnacaniorcid logoMartin Čech avatar Martin Čechorcid logoBjörn Grüning avatar Björn GrüningXi Liu avatar Xi LiuAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBérénice Batut avatar Bérénice Batutorcid logoHelena Rasche avatar Helena RaschePeter-Bram 't Hoen avatar Peter-Bram 't Hoen

Funding

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

References