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:

orcid logoAnthony Bretaudeau avatar Anthony BretaudeauCarlos Chee Mendonça avatar Carlos Chee MendonçaJovana Maksimovic avatar Jovana MaksimovicSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoLucille Delisle avatar Lucille DelisleMatt Ritchie avatar Matt Ritchieorcid logoTeresa Müller avatar Teresa Müllerorcid logoMartin Čech avatar Martin Čechorcid logoToby Hodges avatar Toby Hodgesorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoMorgan Howells avatar Morgan HowellsCharlotte Adang avatar Charlotte Adangorcid logoWendi Bacon avatar Wendi Baconorcid logoPeter van Heusden avatar Peter van HeusdenWilliam Durand avatar William DurandCasper de Visser avatar Casper de Visserorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoSofoklis Keisaris avatar Sofoklis KeisarisChao Zhang avatar Chao ZhangMatthias Bernt avatar Matthias Berntorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoArmin Dadras avatar Armin DadrasXi Liu avatar Xi LiuIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoClemens Blank avatar Clemens Blankorcid logoMo Heydarian avatar Mo Heydarianorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzThorben Stehling avatar Thorben StehlingSimon Bray avatar Simon BrayBelinda Phipson avatar Belinda PhipsonAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiMarkus Wolfien avatar Markus WolfienEkaterina Polkh avatar Ekaterina PolkhShian Su avatar Shian SuPablo Moreno avatar Pablo Morenoorcid logoGraeme Tyson avatar Graeme TysonOlivier Dameron avatar Olivier Dameronorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoErwan Corre avatar Erwan CorreAnne Siegel avatar Anne SiegelDaniel Maticzka avatar Daniel MaticzkaCharity Law avatar Charity LawXavier Garnier avatar Xavier Garnierorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoMatti Hoch avatar Matti HochMehmet Tekman avatar Mehmet TekmanMateusz Kuzak avatar Mateusz KuzakMarius van den Beek avatar Marius van den Beekorcid logoHelena Rasche avatar Helena RascheJames Taylor avatar James TaylorHarriet Dashnow avatar Harriet Dashnoworcid logoMira Kuntz avatar Mira Kuntzorcid logoMaria Doyle avatar Maria Doyleorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoMallory Freeberg avatar Mallory Freebergorcid logoFlorian Heyl avatar Florian Heylorcid logoJulia Jakiela avatar Julia Jakielaorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoLinelle Abueg avatar Linelle AbuegPeter-Bram 't Hoen avatar Peter-Bram 't HoenNiall Beard avatar Niall BeardAnna Trigos avatar Anna Trigosorcid logoBjörn Grüning avatar Björn GrüningAndrea Bagnacani avatar Andrea Bagnacaniorcid logoMateo Boudet avatar Mateo Boudetorcid logoMarisa Loach avatar Marisa LoachJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoSaskia Hiltemann avatar Saskia HiltemannGildas Le Corguillé avatar Gildas Le Corguilléorcid logoBérénice Batut avatar Bérénice Batutorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoClea Siguret avatar Clea Siguret

Funding

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

Logo
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.
Logo
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.
Logo
de.NBI
Logo
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)