transcriptomics

Tutorials covering transcriptomics

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

Proteomics

Lesson Slides Hands-on Recordings Input dataset Workflows
Multiomics data analysis using MultiGSEA
multi-omics transcriptomics proteomics metabolomics

Single Cell

Lesson Slides Hands-on Recordings Input dataset Workflows
Bulk RNA Deconvolution with MuSiC
transcriptomics deconvolution
Comparing inferred cell compositions using MuSiC deconvolution
transcriptomics deconvolution
Evaluating Reference Data for Bulk RNA Deconvolution
transcriptomics deconvolution
Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution
transcriptomics data management deconvolution
Pseudobulk Analysis with Decoupler and EdgeR
transcriptomics pseudobulk

Transcriptomics

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Transcriptomics
Pathway analysis with the MINERVA Platform
bulk rna-seq viz cyoa
Reference-based RNA-Seq data analysis
bulk rna-seq collections drosophila QC cyoa deutsch español italiano
De novo transcriptome reconstruction with RNA-Seq
1: RNA-Seq reads to counts
collections mouse QC
2: RNA-seq counts to genes
limma-voom mouse QC
3: RNA-seq genes to pathways
mouse
CLIP-Seq data analysis from pre-processing to motif detection
Differential abundance testing of small RNAs
GO Enrichment Analysis
Genome-wide alternative splicing analysis
alternative splicing isoform switching
Network analysis with Heinz
metatranscriptomics network analysis
RNA Seq Counts to Viz in R
interactive-tools
RNA-RNA interactome data analysis
RNA-Seq analysis with AskOmics Interactive Tool
RNA-seq Alignment with STAR
Small Non-coding RNA Clustering using BlockClust
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
interactive-tools
Visualization of RNA-Seq results with heatmap2
Whole transcriptome analysis of Arabidopsis thaliana
miRNA plants stress tolerance

Contributors

This material was contributed to by:

orcid logoJulia Jakiela avatar Julia Jakielaorcid logoPavankumar Videm avatar Pavankumar VidemCarlos Chee Mendonça avatar Carlos Chee Mendonçaorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoArmin Dadras avatar Armin Dadrasorcid logoLinelle Abueg avatar Linelle AbuegJovana Maksimovic avatar Jovana Maksimovicorcid logoAnika Erxleben avatar Anika ErxlebenIGC Bioinformatics Unit avatar IGC Bioinformatics UnitJosé Manuel Domínguez avatar José Manuel DomínguezCasper de Visser avatar Casper de VisserPeter-Bram 't Hoen avatar Peter-Bram 't HoenCharlotte Adang avatar Charlotte Adangorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoMatthias Bernt avatar Matthias Berntorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoSaskia Hiltemann avatar Saskia HiltemannAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoErwan Corre avatar Erwan CorreOlivier Dameron avatar Olivier DameronDaniel Maticzka avatar Daniel Maticzkaorcid logoToby Hodges avatar Toby Hodgesorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoChao Zhang avatar Chao ZhangSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoGraeme Tyson avatar Graeme TysonHarriet Dashnow avatar Harriet Dashnoworcid logoMira Kuntz avatar Mira Kuntzorcid logoMarisa Loach avatar Marisa LoachAndrea Bagnacani avatar Andrea BagnacaniSimon Bray avatar Simon Brayorcid logoWendi Bacon avatar Wendi Baconorcid logoCristóbal Gallardo avatar Cristóbal GallardoAnna Trigos avatar Anna Trigosorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoLucille Delisle avatar Lucille Delisleorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoMarius van den Beek avatar Marius van den BeekGildas Le Corguillé avatar Gildas Le CorguilléXi Liu avatar Xi Liuorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoMorgan Howells avatar Morgan Howellsorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMartin Čech avatar Martin Čechorcid logoTeresa Müller avatar Teresa MüllerPablo Moreno avatar Pablo Morenoorcid logoClemens Blank avatar Clemens Blankorcid logoMatti Hoch avatar Matti Hochorcid logoMaria Doyle avatar Maria Doyleorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkWilliam Durand avatar William Durandorcid logoMo Heydarian avatar Mo HeydarianBelinda Phipson avatar Belinda PhipsonMehmet Tekman avatar Mehmet TekmanEkaterina Polkh avatar Ekaterina Polkhorcid logoBérénice Batut avatar Bérénice Batutorcid logoBjörn Grüning avatar Björn Grüningorcid logoDiana Chiang Jurado avatar Diana Chiang JuradoNiall Beard avatar Niall BeardAnne Siegel avatar Anne SiegelMatt Ritchie avatar Matt RitchieCharity Law avatar Charity Laworcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoHelena Rasche avatar Helena Rascheorcid logoFlorian Heyl avatar Florian HeylXavier Garnier avatar Xavier GarnierMateusz Kuzak avatar Mateusz KuzakShian Su avatar Shian SuMarkus Wolfien avatar Markus WolfienJames Taylor avatar James Taylororcid logoClea Siguret avatar Clea SiguretThorben Stehling avatar Thorben Stehlingorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoMateo Boudet avatar Mateo Boudet

Funding

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

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Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.
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de.NBI
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Melbourne Bioinformatics
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BeYond-COVID
BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response. This project has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement № 101046203 (BY-COVID)
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The University of Melbourne
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DASH UK
This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.
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Australian BioCommons