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 logoLucille Delisle avatar Lucille Delisleorcid logoErwan Corre avatar Erwan CorreGildas Le Corguillé avatar Gildas Le CorguilléDaniel Maticzka avatar Daniel Maticzkaorcid logoCristóbal Gallardo avatar Cristóbal GallardoChao Zhang avatar Chao Zhangorcid logoBjörn Grüning avatar Björn Grüningorcid logoPeter van Heusden avatar Peter van HeusdenAndrea Bagnacani avatar Andrea BagnacaniBelinda Phipson avatar Belinda Phipsonorcid logoToby Hodges avatar Toby HodgesMateusz Kuzak avatar Mateusz KuzakIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoClea Siguret avatar Clea Siguretorcid logoMo Heydarian avatar Mo Heydarianorcid logoTeresa Müller avatar Teresa MüllerAnton Nekrutenko avatar Anton NekrutenkoMarkus Wolfien avatar Markus Wolfienorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzCasper de Visser avatar Casper de Visserorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoMallory Freeberg avatar Mallory Freebergorcid logoHelena Rasche avatar Helena RascheJosé Manuel Domínguez avatar José Manuel DomínguezHarriet Dashnow avatar Harriet DashnowXavier Garnier avatar Xavier Garnierorcid logoMaria Doyle avatar Maria DoyleNiall Beard avatar Niall BeardEkaterina Polkh avatar Ekaterina Polkhorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoMatti Hoch avatar Matti Hochorcid logoAnthony Bretaudeau avatar Anthony BretaudeauJames Taylor avatar James Taylororcid logoPavankumar Videm avatar Pavankumar VidemCharlotte Adang avatar Charlotte AdangShian Su avatar Shian Suorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoSofoklis Keisaris avatar Sofoklis KeisarisMehmet Tekman avatar Mehmet Tekmanorcid logoFlorian Heyl avatar Florian Heylorcid logoMateo Boudet avatar Mateo BoudetPeter-Bram 't Hoen avatar Peter-Bram 't HoenAnna Trigos avatar Anna TrigosMarius van den Beek avatar Marius van den Beekorcid logoGraeme Tyson avatar Graeme Tysonorcid logoMartin Čech avatar Martin Čechorcid logoIacopo Cristoferi avatar Iacopo CristoferiMatt Ritchie avatar Matt RitchieOlivier Dameron avatar Olivier Dameronorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkSimon Bray avatar Simon Brayorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoClemens Blank avatar Clemens Blankorcid logoArmin Dadras avatar Armin DadrasJovana Maksimovic avatar Jovana Maksimovicorcid logoBérénice Batut avatar Bérénice BatutWilliam Durand avatar William DurandAnne Siegel avatar Anne Siegelorcid logoWolfgang Maier avatar Wolfgang MaierXi Liu avatar Xi Liuorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMira Kuntz avatar Mira KuntzCharity Law avatar Charity Laworcid logoNicola Soranzo avatar Nicola Soranzoorcid logoLinelle Abueg avatar Linelle AbuegSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulam

Funding

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

References