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

Contributors

This material was contributed to by:

orcid logoNicola Soranzo avatar Nicola SoranzoAnna Trigos avatar Anna Trigosorcid logoErwan Corre avatar Erwan CorreMehmet Tekman avatar Mehmet Tekmanorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiAndrea Bagnacani avatar Andrea Bagnacaniorcid logoPeter van Heusden avatar Peter van HeusdenJovana Maksimovic avatar Jovana Maksimovicorcid logoArmin Dadras avatar Armin Dadrasorcid logoMo Heydarian avatar Mo HeydarianMarius van den Beek avatar Marius van den Beekorcid logoFlorian Heyl avatar Florian Heylorcid logoMira Kuntz avatar Mira KuntzShian Su avatar Shian Suorcid logoTeresa Müller avatar Teresa Müllerorcid logoClemens Blank avatar Clemens Blankorcid logoMatti Hoch avatar Matti Hochorcid logoSaskia Hiltemann avatar Saskia HiltemannBelinda Phipson avatar Belinda PhipsonJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoClea Siguret avatar Clea Siguretorcid logoLucille Delisle avatar Lucille DelisleEkaterina Polkh avatar Ekaterina Polkhorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoLinelle Abueg avatar Linelle Abuegorcid logoBjörn Grüning avatar Björn GrüningChao Zhang avatar Chao Zhangorcid logoGraeme Tyson avatar Graeme Tysonorcid logoToby Hodges avatar Toby Hodgesorcid logoMaria Doyle avatar Maria Doyleorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzMarkus Wolfien avatar Markus WolfienHarriet Dashnow avatar Harriet Dashnoworcid logoBérénice Batut avatar Bérénice Batutorcid logoMallory Freeberg avatar Mallory FreebergMateusz Kuzak avatar Mateusz KuzakIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoCristóbal Gallardo avatar Cristóbal GallardoAnne Siegel avatar Anne Siegelorcid logoAnthony Bretaudeau avatar Anthony BretaudeauGildas Le Corguillé avatar Gildas Le CorguilléCharity Law avatar Charity Laworcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMartin Čech avatar Martin Čechorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosXi Liu avatar Xi LiuMatt Ritchie avatar Matt Ritchieorcid logoAnika Erxleben avatar Anika ErxlebenDaniel Maticzka avatar Daniel Maticzkaorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoIacopo Cristoferi avatar Iacopo CristoferiSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMarek Ostaszewski avatar Marek OstaszewskiWilliam Durand avatar William DurandSimon Bray avatar Simon BrayOlivier Dameron avatar Olivier DameronNiall Beard avatar Niall Beardorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkJames Taylor avatar James Taylororcid logoHelena Rasche avatar Helena Rascheorcid logoMateo Boudet avatar Mateo BoudetXavier Garnier avatar Xavier Garnierorcid logoAnne Fouilloux avatar Anne Fouilloux

Funding

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

References