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
Pseudobulk Analysis with Decoupler and EdgeR
transcriptomics pseudobulk
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

Transcriptomics

Lesson Slides Hands-on Recordings Input dataset Workflows
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
Introduction to Transcriptomics
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
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

Contributors

This material was contributed to by:

Xavier Garnier avatar Xavier GarnierCarlos Chee Mendonça avatar Carlos Chee Mendonçaorcid logoErwan Corre avatar Erwan Correorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoHelena Rasche avatar Helena Rascheorcid logoPeter van Heusden avatar Peter van HeusdenThorben Stehling avatar Thorben StehlingBelinda Phipson avatar Belinda Phipsonorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoBérénice Batut avatar Bérénice BatutPeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoMateo Boudet avatar Mateo Boudetorcid logoWendi Bacon avatar Wendi Baconorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzXi Liu avatar Xi Liuorcid logoMaria Doyle avatar Maria DoyleGildas Le Corguillé avatar Gildas Le Corguilléorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMallory Freeberg avatar Mallory Freebergorcid logoSaskia Hiltemann avatar Saskia HiltemannAnne Siegel avatar Anne Siegelorcid logoFlorian Heyl avatar Florian Heylorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoArmin Dadras avatar Armin Dadrasorcid logoClea Siguret avatar Clea SiguretSimon Bray avatar Simon Brayorcid logoGraeme Tyson avatar Graeme Tysonorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosCharlotte Adang avatar Charlotte AdangJovana Maksimovic avatar Jovana MaksimovicJames Taylor avatar James Taylororcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoPavankumar Videm avatar Pavankumar VidemCharity Law avatar Charity Laworcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMorgan Howells avatar Morgan HowellsOlivier Dameron avatar Olivier Dameronorcid logoMatti Hoch avatar Matti HochAndrea Bagnacani avatar Andrea Bagnacaniorcid logoJulia Jakiela avatar Julia JakielaSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamMarius van den Beek avatar Marius van den BeekShian Su avatar Shian Suorcid logoMarek Ostaszewski avatar Marek OstaszewskiAnna Trigos avatar Anna Trigosorcid logoTeresa Müller avatar Teresa MüllerMateusz Kuzak avatar Mateusz Kuzakorcid logoDiana Chiang Jurado avatar Diana Chiang JuradoPablo Moreno avatar Pablo MorenoHarriet Dashnow avatar Harriet DashnowMatt Ritchie avatar Matt Ritchieorcid logoMira Kuntz avatar Mira KuntzCasper de Visser avatar Casper de VisserJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoBjörn Grüning avatar Björn Grüningorcid logoMarisa Loach avatar Marisa Loachorcid logoLucille Delisle avatar Lucille DelisleIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoClemens Blank avatar Clemens BlankWilliam Durand avatar William DurandDaniel Maticzka avatar Daniel Maticzkaorcid logoIacopo Cristoferi avatar Iacopo CristoferiMarkus Wolfien avatar Markus Wolfienorcid logoMo Heydarian avatar Mo HeydarianMatthias Bernt avatar Matthias BerntChao Zhang avatar Chao ZhangMehmet Tekman avatar Mehmet TekmanNiall Beard avatar Niall Beardorcid logoMartin Čech avatar Martin ČechAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoEkaterina Polkh avatar Ekaterina Polkhorcid logoToby Hodges avatar Toby Hodgesorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoLinelle Abueg avatar Linelle Abueg

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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Australian BioCommons
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Melbourne Bioinformatics
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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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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)