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:

Xi Liu avatar Xi LiuNiall Beard avatar Niall BeardPeter-Bram 't Hoen avatar Peter-Bram 't HoenSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamMarius van den Beek avatar Marius van den BeekMarkus Wolfien avatar Markus Wolfienorcid logoToby Hodges avatar Toby HodgesAnna Trigos avatar Anna Trigosorcid logoWolfgang Maier avatar Wolfgang MaierDaniel Maticzka avatar Daniel Maticzkaorcid logoTeresa Müller avatar Teresa MüllerShian Su avatar Shian SuAndrea Bagnacani avatar Andrea Bagnacaniorcid logoMallory Freeberg avatar Mallory Freebergorcid logoArmin Dadras avatar Armin DadrasJames Taylor avatar James TaylorMatt Ritchie avatar Matt Ritchieorcid logoBérénice Batut avatar Bérénice Batutorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMatti Hoch avatar Matti HochOlivier Dameron avatar Olivier Dameronorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzAnton Nekrutenko avatar Anton NekrutenkoCharity Law avatar Charity Laworcid logoAnne Fouilloux avatar Anne FouillouxJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoBjörn Grüning avatar Björn Grüningorcid logoClea Siguret avatar Clea Siguretorcid logoPavankumar Videm avatar Pavankumar VidemXavier Garnier avatar Xavier GarnierCasper de Visser avatar Casper de Visserorcid logoFlorian Heyl avatar Florian Heylorcid logoMo Heydarian avatar Mo Heydarianorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiEkaterina Polkh avatar Ekaterina PolkhChao Zhang avatar Chao Zhangorcid logoAnthony Bretaudeau avatar Anthony BretaudeauMehmet Tekman avatar Mehmet TekmanBelinda Phipson avatar Belinda Phipsonorcid logoGraeme Tyson avatar Graeme Tysonorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosSimon Bray avatar Simon Brayorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoClemens Blank avatar Clemens Blankorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoSofoklis Keisaris avatar Sofoklis KeisarisGildas Le Corguillé avatar Gildas Le CorguilléMateusz Kuzak avatar Mateusz Kuzakorcid logoMateo Boudet avatar Mateo Boudetorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoLinelle Abueg avatar Linelle Abuegorcid logoMira Kuntz avatar Mira KuntzIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoErwan Corre avatar Erwan Correorcid logoLucille Delisle avatar Lucille DelisleJovana Maksimovic avatar Jovana MaksimovicHarriet Dashnow avatar Harriet Dashnoworcid logoAnika Erxleben avatar Anika Erxlebenorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoHelena Rasche avatar Helena Rascheorcid logoMaria Doyle avatar Maria DoyleCharlotte Adang avatar Charlotte Adangorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoNicola Soranzo avatar Nicola SoranzoAnne Siegel avatar Anne Siegelorcid logoMartin Čech avatar Martin ČechWilliam Durand avatar William Durand

Funding

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

References