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.

Follow topic updates rss-feed with our RSS Feed

Community Resources

Community Home Maintainer Home

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 logoLucille Delisle avatar Lucille Delisleorcid logoFlorian Heyl avatar Florian HeylSimon Bray avatar Simon Brayorcid logoMartin Čech avatar Martin ČechPeter-Bram 't Hoen avatar Peter-Bram 't HoenMarkus Wolfien avatar Markus WolfienAnne Siegel avatar Anne Siegelorcid logoClea Siguret avatar Clea Siguretorcid logoToby Hodges avatar Toby Hodgesorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoAnna Trigos avatar Anna TrigosOlivier Dameron avatar Olivier Dameronorcid logoArmin Dadras avatar Armin DadrasMateusz Kuzak avatar Mateusz KuzakMatt Ritchie avatar Matt Ritchieorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoBérénice Batut avatar Bérénice Batutorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoMo Heydarian avatar Mo Heydarianorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoWolfgang Maier avatar Wolfgang MaierJames Taylor avatar James TaylorJovana Maksimovic avatar Jovana Maksimovicorcid logoSaskia Hiltemann avatar Saskia HiltemannMarius van den Beek avatar Marius van den Beekorcid logoClemens Blank avatar Clemens Blankorcid logoMateo Boudet avatar Mateo Boudetorcid logoGraeme Tyson avatar Graeme TysonNiall Beard avatar Niall BeardCharlotte Adang avatar Charlotte Adangorcid logoLinelle Abueg avatar Linelle Abuegorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoTeresa Müller avatar Teresa Müllerorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnne Fouilloux avatar Anne FouillouxXi Liu avatar Xi LiuWilliam Durand avatar William Durandorcid logoMatti Hoch avatar Matti HochAnton Nekrutenko avatar Anton NekrutenkoShian Su avatar Shian SuBelinda Phipson avatar Belinda PhipsonChao Zhang avatar Chao ZhangDaniel Maticzka avatar Daniel Maticzkaorcid logoIacopo Cristoferi avatar Iacopo CristoferiCasper de Visser avatar Casper de Visserorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoBjörn Grüning avatar Björn Grüningorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMira Kuntz avatar Mira Kuntzorcid logoErwan Corre avatar Erwan CorreGildas Le Corguillé avatar Gildas Le CorguilléAndrea Bagnacani avatar Andrea Bagnacaniorcid logoNicola Soranzo avatar Nicola SoranzoXavier Garnier avatar Xavier GarnierIGC Bioinformatics Unit avatar IGC Bioinformatics UnitEkaterina Polkh avatar Ekaterina Polkhorcid logoHelena Rasche avatar Helena RascheJosé Manuel Domínguez avatar José Manuel DomínguezHarriet Dashnow avatar Harriet DashnowCharity Law avatar Charity LawMehmet Tekman avatar Mehmet TekmanSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoMaria Doyle avatar Maria Doyle

Funding

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

References