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

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:

orcid logoMartin Čech avatar Martin Čechorcid logoMira Kuntz avatar Mira Kuntzorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoArmin Dadras avatar Armin Dadrasorcid logoWolfgang Maier avatar Wolfgang MaierMarius van den Beek avatar Marius van den Beekorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosAnna Trigos avatar Anna TrigosIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoAnne Fouilloux avatar Anne FouillouxSimon Bray avatar Simon Brayorcid logoLucille Delisle avatar Lucille Delisleorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoMaria Doyle avatar Maria DoyleXi Liu avatar Xi LiuEkaterina Polkh avatar Ekaterina Polkhorcid logoJulia Jakiela avatar Julia JakielaCarlos Chee Mendonça avatar Carlos Chee MendonçaOlivier Dameron avatar Olivier Dameronorcid logoGraeme Tyson avatar Graeme TysonShian Su avatar Shian SuAndrea Bagnacani avatar Andrea Bagnacaniorcid logoToby Hodges avatar Toby Hodgesorcid logoErwan Corre avatar Erwan Correorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoWendi Bacon avatar Wendi BaconMatthias Bernt avatar Matthias BerntJames Taylor avatar James TaylorMehmet Tekman avatar Mehmet TekmanMateusz Kuzak avatar Mateusz KuzakCharity Law avatar Charity LawJovana Maksimovic avatar Jovana MaksimovicHarriet Dashnow avatar Harriet DashnowAnne Siegel avatar Anne Siegelorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMarek Ostaszewski avatar Marek OstaszewskiMarkus Wolfien avatar Markus Wolfienorcid logoIacopo Cristoferi avatar Iacopo CristoferiSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamAnton Nekrutenko avatar Anton NekrutenkoDaniel Maticzka avatar Daniel Maticzkaorcid logoMo Heydarian avatar Mo Heydarianorcid logoPeter van Heusden avatar Peter van HeusdenPeter-Bram 't Hoen avatar Peter-Bram 't HoenGildas Le Corguillé avatar Gildas Le Corguilléorcid logoLinelle Abueg avatar Linelle Abuegorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoMallory Freeberg avatar Mallory Freebergorcid logoHelena Rasche avatar Helena Rascheorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoPavankumar Videm avatar Pavankumar VidemXavier Garnier avatar Xavier GarnierBelinda Phipson avatar Belinda PhipsonThorben Stehling avatar Thorben Stehlingorcid logoMarisa Loach avatar Marisa Loachorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoBjörn Grüning avatar Björn GrüningCasper de Visser avatar Casper de VisserCharlotte Adang avatar Charlotte Adangorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoFlorian Heyl avatar Florian HeylMatt Ritchie avatar Matt Ritchieorcid logoBérénice Batut avatar Bérénice Batutorcid logoClea Siguret avatar Clea Siguretorcid logoMorgan Howells avatar Morgan Howellsorcid logoMateo Boudet avatar Mateo BoudetJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoMatti Hoch avatar Matti HochWilliam Durand avatar William Durandorcid logoClemens Blank avatar Clemens BlankChao Zhang avatar Chao Zhangorcid logoSofoklis Keisaris avatar Sofoklis KeisarisPablo Moreno avatar Pablo Morenoorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoTeresa Müller avatar Teresa MüllerNiall Beard avatar Niall Beard

Funding

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

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de.NBI
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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)
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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.