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 logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiMarkus Wolfien avatar Markus Wolfienorcid logoSofoklis Keisaris avatar Sofoklis KeisarisXi Liu avatar Xi Liuorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosMateusz Kuzak avatar Mateusz Kuzakorcid logoToby Hodges avatar Toby Hodgesorcid logoMo Heydarian avatar Mo HeydarianIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoMateo Boudet avatar Mateo BoudetAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMorgan Howells avatar Morgan Howellsorcid logoWolfgang Maier avatar Wolfgang MaierCasper de Visser avatar Casper de Visserorcid logoMartin Čech avatar Martin Čechorcid logoBérénice Batut avatar Bérénice BatutMatt Ritchie avatar Matt RitchieJovana Maksimovic avatar Jovana Maksimovicorcid logoMarek Ostaszewski avatar Marek OstaszewskiMarius van den Beek avatar Marius van den BeekSimon Bray avatar Simon BrayPablo Moreno avatar Pablo Morenoorcid logoClea Siguret avatar Clea SiguretAnne Siegel avatar Anne Siegelorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoErwan Corre avatar Erwan Correorcid logoMarisa Loach avatar Marisa Loachorcid logoMaria Doyle avatar Maria Doyleorcid logoMatti Hoch avatar Matti HochCarlos Chee Mendonça avatar Carlos Chee MendonçaHarriet Dashnow avatar Harriet Dashnoworcid logoClemens Blank avatar Clemens BlankDaniel Maticzka avatar Daniel MaticzkaJosé Manuel Domínguez avatar José Manuel DomínguezWilliam Durand avatar William Durandorcid logoHelena Rasche avatar Helena Rascheorcid logoTeresa Müller avatar Teresa MüllerAnna Trigos avatar Anna TrigosCharity Law avatar Charity Laworcid logoAnika Erxleben avatar Anika Erxlebenorcid logoNicola Soranzo avatar Nicola SoranzoPeter-Bram 't Hoen avatar Peter-Bram 't HoenJames Taylor avatar James TaylorEkaterina Polkh avatar Ekaterina PolkhChao Zhang avatar Chao ZhangGildas Le Corguillé avatar Gildas Le Corguilléorcid logoMira Kuntz avatar Mira KuntzThorben Stehling avatar Thorben StehlingMatthias Bernt avatar Matthias BerntOlivier Dameron avatar Olivier DameronSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamCharlotte Adang avatar Charlotte Adangorcid logoWendi Bacon avatar Wendi BaconNiall Beard avatar Niall BeardAndrea Bagnacani avatar Andrea BagnacaniXavier Garnier avatar Xavier GarnierMehmet Tekman avatar Mehmet Tekmanorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoBjörn Grüning avatar Björn Grüningorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoShian Su avatar Shian Suorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzBelinda Phipson avatar Belinda Phipsonorcid logoArmin Dadras avatar Armin Dadrasorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoGraeme Tyson avatar Graeme Tysonorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoMallory Freeberg avatar Mallory Freebergorcid logoLinelle Abueg avatar Linelle Abuegorcid logoJulia Jakiela avatar Julia Jakielaorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoLucille Delisle avatar Lucille Delisleorcid logoFlorian Heyl avatar Florian Heyl

Funding

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

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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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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.