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 logoFlorian Heyl avatar Florian Heylorcid logoGraeme Tyson avatar Graeme Tysonorcid logoArmin Dadras avatar Armin DadrasXi Liu avatar Xi Liuorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosAnna Trigos avatar Anna Trigosorcid logoMartin Čech avatar Martin Čechorcid logoMaria Doyle avatar Maria Doyleorcid logoBjörn Grüning avatar Björn Grüningorcid logoSofoklis Keisaris avatar Sofoklis KeisarisIGC Bioinformatics Unit avatar IGC Bioinformatics UnitSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamSimon Bray avatar Simon Brayorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoErwan Corre avatar Erwan CorreMarius van den Beek avatar Marius van den BeekChao Zhang avatar Chao ZhangMateusz Kuzak avatar Mateusz KuzakGildas Le Corguillé avatar Gildas Le CorguilléShian Su avatar Shian SuCharity Law avatar Charity LawCharlotte Adang avatar Charlotte Adangorcid logoClea Siguret avatar Clea Siguretorcid logoLinelle Abueg avatar Linelle AbuegDaniel Maticzka avatar Daniel MaticzkaAnne Siegel avatar Anne Siegelorcid logoAnne Fouilloux avatar Anne FouillouxNiall Beard avatar Niall Beardorcid logoAnika Erxleben avatar Anika ErxlebenAnton Nekrutenko avatar Anton Nekrutenkoorcid logoPeter van Heusden avatar Peter van HeusdenHarriet Dashnow avatar Harriet Dashnoworcid logoPavankumar Videm avatar Pavankumar Videmorcid logoMarek Ostaszewski avatar Marek OstaszewskiMarkus Wolfien avatar Markus WolfienPeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiCasper de Visser avatar Casper de Visserorcid logoMallory Freeberg avatar Mallory Freebergorcid logoIacopo Cristoferi avatar Iacopo CristoferiWilliam Durand avatar William DurandJames Taylor avatar James Taylororcid logoMira Kuntz avatar Mira Kuntzorcid logoMatti Hoch avatar Matti HochMehmet Tekman avatar Mehmet TekmanXavier Garnier avatar Xavier Garnierorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMateo Boudet avatar Mateo Boudetorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoClemens Blank avatar Clemens Blankorcid logoLucille Delisle avatar Lucille DelisleAndrea Bagnacani avatar Andrea Bagnacaniorcid logoHelena Rasche avatar Helena RascheMatt Ritchie avatar Matt RitchieEkaterina Polkh avatar Ekaterina Polkhorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoBérénice Batut avatar Bérénice Batutorcid logoTeresa Müller avatar Teresa Müllerorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMo Heydarian avatar Mo HeydarianJovana Maksimovic avatar Jovana MaksimovicJosé Manuel Domínguez avatar José Manuel DomínguezBelinda Phipson avatar Belinda PhipsonOlivier Dameron avatar Olivier Dameronorcid logoToby Hodges avatar Toby Hodges

Funding

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

References