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:

Casper de Visser avatar Casper de Visserorcid logoBérénice Batut avatar Bérénice Batutorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiShian Su avatar Shian SuJovana Maksimovic avatar Jovana MaksimovicAnne Siegel avatar Anne SiegelMarius van den Beek avatar Marius van den Beekorcid logoMartin Čech avatar Martin Čechorcid logoAnne Fouilloux avatar Anne FouillouxNiall Beard avatar Niall Beardorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoToby Hodges avatar Toby HodgesSimon Bray avatar Simon Brayorcid logoGraeme Tyson avatar Graeme Tysonorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoErwan Corre avatar Erwan Correorcid logoClea Siguret avatar Clea SiguretOlivier Dameron avatar Olivier Dameronorcid logoWolfgang Maier avatar Wolfgang MaierMatt Ritchie avatar Matt Ritchieorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzEkaterina Polkh avatar Ekaterina Polkhorcid logoBjörn Grüning avatar Björn Grüningorcid logoTeresa Müller avatar Teresa MüllerAnna Trigos avatar Anna Trigosorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoNicola Soranzo avatar Nicola SoranzoPeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoPavankumar Videm avatar Pavankumar VidemDaniel Maticzka avatar Daniel MaticzkaCharlotte Adang avatar Charlotte AdangJames Taylor avatar James Taylororcid logoSofoklis Keisaris avatar Sofoklis KeisarisMarkus Wolfien avatar Markus Wolfienorcid logoAnthony Bretaudeau avatar Anthony BretaudeauJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoArmin Dadras avatar Armin Dadrasorcid logoMateo Boudet avatar Mateo BoudetChao Zhang avatar Chao Zhangorcid logoLinelle Abueg avatar Linelle AbuegMateusz Kuzak avatar Mateusz Kuzakorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkAnton Nekrutenko avatar Anton Nekrutenkoorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoPeter van Heusden avatar Peter van HeusdenCharity Law avatar Charity LawBelinda Phipson avatar Belinda PhipsonIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoMatti Hoch avatar Matti Hochorcid logoMira Kuntz avatar Mira KuntzHarriet Dashnow avatar Harriet DashnowWilliam Durand avatar William DurandAndrea Bagnacani avatar Andrea Bagnacaniorcid logoMallory Freeberg avatar Mallory FreebergGildas Le Corguillé avatar Gildas Le Corguilléorcid logoHelena Rasche avatar Helena Rascheorcid logoMaria Doyle avatar Maria Doyleorcid logoFlorian Heyl avatar Florian Heylorcid logoClemens Blank avatar Clemens Blankorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoMo Heydarian avatar Mo Heydarianorcid logoLucille Delisle avatar Lucille DelisleXavier Garnier avatar Xavier GarnierXi Liu avatar Xi LiuMehmet Tekman avatar Mehmet Tekman

Funding

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

References