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 logoLinelle Abueg avatar Linelle AbuegSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamMarius van den Beek avatar Marius van den BeekMehmet Tekman avatar Mehmet TekmanAndrea Bagnacani avatar Andrea Bagnacaniorcid logoHelena Rasche avatar Helena Rascheorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoPeter van Heusden avatar Peter van HeusdenAnna Trigos avatar Anna Trigosorcid logoBjörn Grüning avatar Björn Grüningorcid logoMatti Hoch avatar Matti HochJames Taylor avatar James Taylororcid logoMallory Freeberg avatar Mallory FreebergAnne Siegel avatar Anne SiegelIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoGraeme Tyson avatar Graeme Tysonorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoAnthony Bretaudeau avatar Anthony BretaudeauJovana Maksimovic avatar Jovana MaksimovicXavier Garnier avatar Xavier Garnierorcid logoMaria Doyle avatar Maria DoyleGildas Le Corguillé avatar Gildas Le CorguilléMateusz Kuzak avatar Mateusz Kuzakorcid logoErwan Corre avatar Erwan CorreShian Su avatar Shian Suorcid logoTeresa Müller avatar Teresa MüllerHarriet Dashnow avatar Harriet Dashnoworcid logoMira Kuntz avatar Mira KuntzMatt Ritchie avatar Matt Ritchieorcid logoToby Hodges avatar Toby Hodgesorcid logoClemens Blank avatar Clemens BlankNiall Beard avatar Niall Beardorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosAnton Nekrutenko avatar Anton NekrutenkoChao Zhang avatar Chao Zhangorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMo Heydarian avatar Mo Heydarianorcid logoMartin Čech avatar Martin Čechorcid logoFlorian Heyl avatar Florian HeylCharlotte Adang avatar Charlotte Adangorcid logoArmin Dadras avatar Armin Dadrasorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoClea Siguret avatar Clea SiguretPeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoBérénice Batut avatar Bérénice BatutXi Liu avatar Xi Liuorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiWilliam Durand avatar William Durandorcid logoLucille Delisle avatar Lucille Delisleorcid logoCristóbal Gallardo avatar Cristóbal GallardoEkaterina Polkh avatar Ekaterina PolkhDaniel Maticzka avatar Daniel MaticzkaOlivier Dameron avatar Olivier DameronMarkus Wolfien avatar Markus WolfienCharity Law avatar Charity Laworcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkBelinda Phipson avatar Belinda Phipsonorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoSaskia Hiltemann avatar Saskia HiltemannSimon Bray avatar Simon BrayCasper de Visser avatar Casper de VisserJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoMateo Boudet avatar Mateo Boudetorcid logoAnika Erxleben avatar Anika Erxleben

Funding

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

References