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 logoAnthony Bretaudeau avatar Anthony BretaudeauDaniel Maticzka avatar Daniel Maticzkaorcid logoMaria Doyle avatar Maria Doyleorcid logoErwan Corre avatar Erwan CorreThorben Stehling avatar Thorben Stehlingorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoArmin Dadras avatar Armin Dadrasorcid logoIacopo Cristoferi avatar Iacopo CristoferiWilliam Durand avatar William Durandorcid logoMartin Čech avatar Martin ČechGildas Le Corguillé avatar Gildas Le Corguilléorcid logoMatti Hoch avatar Matti HochNiall Beard avatar Niall BeardXavier Garnier avatar Xavier Garnierorcid logoMira Kuntz avatar Mira Kuntzorcid logoMarisa Loach avatar Marisa Loachorcid logoBjörn Grüning avatar Björn GrüningCasper de Visser avatar Casper de VisserChao Zhang avatar Chao Zhangorcid logoTeresa Müller avatar Teresa MüllerIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoLinelle Abueg avatar Linelle AbuegMatt Ritchie avatar Matt RitchieJames Taylor avatar James Taylororcid logoPeter van Heusden avatar Peter van HeusdenMateusz Kuzak avatar Mateusz KuzakCharlotte Adang avatar Charlotte AdangEkaterina Polkh avatar Ekaterina PolkhMehmet Tekman avatar Mehmet Tekmanorcid logoLucille Delisle avatar Lucille Delisleorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoMo Heydarian avatar Mo Heydarianorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoMatthias Bernt avatar Matthias Berntorcid logoClea Siguret avatar Clea SiguretMarkus Wolfien avatar Markus WolfienAndrea Bagnacani avatar Andrea Bagnacaniorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoToby Hodges avatar Toby HodgesSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoMarius van den Beek avatar Marius van den BeekPeter-Bram 't Hoen avatar Peter-Bram 't HoenAnna Trigos avatar Anna TrigosJosé Manuel Domínguez avatar José Manuel DomínguezXi Liu avatar Xi LiuBelinda Phipson avatar Belinda PhipsonJovana Maksimovic avatar Jovana Maksimovicorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoGraeme Tyson avatar Graeme Tysonorcid logoJulia Jakiela avatar Julia JakielaAnne Siegel avatar Anne SiegelAnton Nekrutenko avatar Anton NekrutenkoShian Su avatar Shian SuPablo Moreno avatar Pablo Morenoorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoMorgan Howells avatar Morgan Howellsorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoHelena Rasche avatar Helena Rascheorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiOlivier Dameron avatar Olivier DameronHarriet Dashnow avatar Harriet Dashnoworcid logoMallory Freeberg avatar Mallory Freebergorcid logoBérénice Batut avatar Bérénice Batutorcid logoFlorian Heyl avatar Florian HeylCarlos Chee Mendonça avatar Carlos Chee Mendonçaorcid logoMateo Boudet avatar Mateo BoudetSimon Bray avatar Simon Brayorcid logoNicola Soranzo avatar Nicola SoranzoCharity Law avatar Charity Laworcid logoWendi Bacon avatar Wendi Baconorcid logoClemens Blank avatar Clemens Blank

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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Melbourne Bioinformatics
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Australian BioCommons
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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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de.NBI
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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