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:

orcid logoMira Kuntz avatar Mira KuntzMatt Ritchie avatar Matt Ritchieorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosMarius van den Beek avatar Marius van den BeekSimon Bray avatar Simon Brayorcid logoBérénice Batut avatar Bérénice BatutIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoBjörn Grüning avatar Björn GrüningJosé Manuel Domínguez avatar José Manuel DomínguezCharity Law avatar Charity LawCharlotte Adang avatar Charlotte Adangorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoMallory Freeberg avatar Mallory FreebergNiall Beard avatar Niall BeardAnton Nekrutenko avatar Anton NekrutenkoXavier Garnier avatar Xavier GarnierWilliam Durand avatar William Durandorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoMateo Boudet avatar Mateo Boudetorcid logoMo Heydarian avatar Mo Heydarianorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiAndrea Bagnacani avatar Andrea BagnacaniMehmet Tekman avatar Mehmet Tekmanorcid logoMatti Hoch avatar Matti HochXi Liu avatar Xi Liuorcid logoAnika Erxleben avatar Anika ErxlebenJovana Maksimovic avatar Jovana Maksimovicorcid logoLinelle Abueg avatar Linelle Abuegorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoFlorian Heyl avatar Florian Heylorcid logoToby Hodges avatar Toby Hodgesorcid logoErwan Corre avatar Erwan CorreSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoMartin Čech avatar Martin ČechGildas Le Corguillé avatar Gildas Le CorguilléMateusz Kuzak avatar Mateusz Kuzakorcid logoMaria Doyle avatar Maria DoyleEkaterina Polkh avatar Ekaterina Polkhorcid logoHelena Rasche avatar Helena Rascheorcid logoNicola Soranzo avatar Nicola SoranzoShian Su avatar Shian Suorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMarek Ostaszewski avatar Marek OstaszewskiPeter-Bram 't Hoen avatar Peter-Bram 't HoenDaniel Maticzka avatar Daniel Maticzkaorcid logoArmin Dadras avatar Armin DadrasAnne Siegel avatar Anne Siegelorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkJames Taylor avatar James TaylorMarkus Wolfien avatar Markus WolfienOlivier Dameron avatar Olivier Dameronorcid logoClemens Blank avatar Clemens BlankBelinda Phipson avatar Belinda PhipsonChao Zhang avatar Chao Zhangorcid logoTeresa Müller avatar Teresa Müllerorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoCasper de Visser avatar Casper de Visserorcid logoClea Siguret avatar Clea SiguretAnna Trigos avatar Anna Trigosorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoLucille Delisle avatar Lucille Delisleorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzHarriet Dashnow avatar Harriet Dashnoworcid logoGraeme Tyson avatar Graeme Tyson

Funding

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

References