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 logoWolfgang Maier avatar Wolfgang Maierorcid logoPavankumar Videm avatar Pavankumar VidemMarkus Wolfien avatar Markus Wolfienorcid logoHelena Rasche avatar Helena Rascheorcid logoMateo Boudet avatar Mateo Boudetorcid logoAnne Fouilloux avatar Anne FouillouxBelinda Phipson avatar Belinda Phipsonorcid logoMira Kuntz avatar Mira KuntzChao Zhang avatar Chao Zhangorcid logoMartin Čech avatar Martin ČechAnton Nekrutenko avatar Anton Nekrutenkoorcid logoNicola Soranzo avatar Nicola SoranzoDaniel Maticzka avatar Daniel Maticzkaorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoFlorian Heyl avatar Florian Heylorcid logoMatti Hoch avatar Matti HochSimon Bray avatar Simon BrayPeter-Bram 't Hoen avatar Peter-Bram 't HoenEkaterina Polkh avatar Ekaterina Polkhorcid logoMallory Freeberg avatar Mallory Freebergorcid logoBérénice Batut avatar Bérénice BatutXavier Garnier avatar Xavier GarnierCharlotte Adang avatar Charlotte AdangAnne Siegel avatar Anne Siegelorcid logoClea Siguret avatar Clea Siguretorcid logoClemens Blank avatar Clemens Blankorcid logoErwan Corre avatar Erwan CorreCasper de Visser avatar Casper de Visserorcid logoToby Hodges avatar Toby Hodgesorcid logoLucille Delisle avatar Lucille DelisleJames Taylor avatar James Taylororcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoMatt Ritchie avatar Matt Ritchieorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoMaria Doyle avatar Maria Doyleorcid logoBjörn Grüning avatar Björn GrüningAndrea Bagnacani avatar Andrea BagnacaniOlivier Dameron avatar Olivier DameronNiall Beard avatar Niall Beardorcid logoMo Heydarian avatar Mo Heydarianorcid logoCristóbal Gallardo avatar Cristóbal GallardoGildas Le Corguillé avatar Gildas Le CorguilléJovana Maksimovic avatar Jovana Maksimovicorcid logoSofoklis Keisaris avatar Sofoklis KeisarisMarius van den Beek avatar Marius van den BeekShian Su avatar Shian Suorcid logoTeresa Müller avatar Teresa Müllerorcid logoSaskia Hiltemann avatar Saskia HiltemannXi Liu avatar Xi LiuWilliam Durand avatar William Durandorcid logoLinelle Abueg avatar Linelle AbuegAnna Trigos avatar Anna TrigosHarriet Dashnow avatar Harriet Dashnoworcid logoArmin Dadras avatar Armin DadrasSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamCharity Law avatar Charity Laworcid logoGraeme Tyson avatar Graeme TysonMehmet Tekman avatar Mehmet TekmanMateusz Kuzak avatar Mateusz Kuzakorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoAnthony Bretaudeau avatar Anthony BretaudeauJosé Manuel Domínguez avatar José Manuel DomínguezIGC Bioinformatics Unit avatar IGC Bioinformatics Unit

Funding

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

References