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 VidemJovana Maksimovic avatar Jovana MaksimovicCasper de Visser avatar Casper de VisserPeter-Bram 't Hoen avatar Peter-Bram 't HoenJames Taylor avatar James Taylororcid logoNicola Soranzo avatar Nicola SoranzoChao Zhang avatar Chao Zhangorcid logoMo Heydarian avatar Mo Heydarianorcid logoToby Hodges avatar Toby Hodgesorcid logoBérénice Batut avatar Bérénice BatutAnne Siegel avatar Anne Siegelorcid logoMaria Doyle avatar Maria DoyleJosé Manuel Domínguez avatar José Manuel DomínguezHarriet Dashnow avatar Harriet Dashnoworcid logoClemens Blank avatar Clemens BlankShian Su avatar Shian SuAnton Nekrutenko avatar Anton Nekrutenkoorcid logoClea Siguret avatar Clea Siguretorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkDaniel Maticzka avatar Daniel MaticzkaBelinda Phipson avatar Belinda Phipsonorcid logoMateo Boudet avatar Mateo Boudetorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamOlivier Dameron avatar Olivier Dameronorcid logoCristóbal Gallardo avatar Cristóbal GallardoCharity Law avatar Charity LawMatt Ritchie avatar Matt RitchieSimon Bray avatar Simon BrayAndrea Bagnacani avatar Andrea BagnacaniMateusz Kuzak avatar Mateusz Kuzakorcid logoAnika Erxleben avatar Anika ErxlebenMarius van den Beek avatar Marius van den Beekorcid logoLucille Delisle avatar Lucille Delisleorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoGraeme Tyson avatar Graeme Tysonorcid logoHelena Rasche avatar Helena RascheEkaterina Polkh avatar Ekaterina PolkhXavier Garnier avatar Xavier GarnierNiall Beard avatar Niall Beardorcid logoMartin Čech avatar Martin ČechAnna Trigos avatar Anna TrigosWilliam Durand avatar William Durandorcid logoMira Kuntz avatar Mira Kuntzorcid logoAnthony Bretaudeau avatar Anthony BretaudeauGildas Le Corguillé avatar Gildas Le Corguilléorcid logoMatti Hoch avatar Matti HochMehmet Tekman avatar Mehmet Tekmanorcid logoErwan Corre avatar Erwan Correorcid logoBjörn Grüning avatar Björn Grüningorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoMallory Freeberg avatar Mallory Freebergorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoLinelle Abueg avatar Linelle AbuegCharlotte Adang avatar Charlotte AdangIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoMarek Ostaszewski avatar Marek OstaszewskiXi Liu avatar Xi Liuorcid logoTeresa Müller avatar Teresa Müllerorcid logoArmin Dadras avatar Armin DadrasMarkus Wolfien avatar Markus Wolfienorcid logoFlorian Heyl avatar Florian Heylorcid logoAnne Fouilloux avatar Anne Fouilloux

Funding

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

References