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:

Charity Law avatar Charity LawAnton Nekrutenko avatar Anton NekrutenkoSimon Bray avatar Simon Brayorcid logoClemens Blank avatar Clemens BlankPablo Moreno avatar Pablo MorenoAnna Trigos avatar Anna Trigosorcid logoNicola Soranzo avatar Nicola SoranzoCarlos Chee Mendonça avatar Carlos Chee Mendonçaorcid logoTeresa Müller avatar Teresa Müllerorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzThorben Stehling avatar Thorben StehlingNiall Beard avatar Niall BeardCasper de Visser avatar Casper de Visserorcid logoAnika Erxleben avatar Anika ErxlebenJosé Manuel Domínguez avatar José Manuel DomínguezMateusz Kuzak avatar Mateusz Kuzakorcid logoPeter van Heusden avatar Peter van HeusdenShian Su avatar Shian Suorcid logoDiana Chiang Jurado avatar Diana Chiang JuradoXavier Garnier avatar Xavier GarnierJames Taylor avatar James TaylorCharlotte Adang avatar Charlotte AdangAndrea Bagnacani avatar Andrea Bagnacaniorcid logoErwan Corre avatar Erwan CorreAnne Siegel avatar Anne Siegelorcid logoArmin Dadras avatar Armin DadrasBelinda Phipson avatar Belinda Phipsonorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoLinelle Abueg avatar Linelle Abuegorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoMaria Doyle avatar Maria DoyleOlivier Dameron avatar Olivier Dameronorcid logoSofoklis Keisaris avatar Sofoklis KeisarisPeter-Bram 't Hoen avatar Peter-Bram 't HoenMatthias Bernt avatar Matthias Berntorcid logoHelena Rasche avatar Helena RascheMarkus Wolfien avatar Markus WolfienChao Zhang avatar Chao Zhangorcid logoMallory Freeberg avatar Mallory Freebergorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoJovana Maksimovic avatar Jovana Maksimovicorcid logoMira Kuntz avatar Mira KuntzMehmet Tekman avatar Mehmet Tekmanorcid logoWendi Bacon avatar Wendi Baconorcid logoGraeme Tyson avatar Graeme TysonXi Liu avatar Xi Liuorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoBjörn Grüning avatar Björn Grüningorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoJulia Jakiela avatar Julia Jakielaorcid logoAnthony Bretaudeau avatar Anthony BretaudeauWilliam Durand avatar William Durandorcid logoToby Hodges avatar Toby HodgesGildas Le Corguillé avatar Gildas Le CorguilléMatt Ritchie avatar Matt Ritchieorcid logoAnne Fouilloux avatar Anne FouillouxDaniel Maticzka avatar Daniel MaticzkaMarius van den Beek avatar Marius van den BeekIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoMartin Čech avatar Martin Čechorcid logoMatti Hoch avatar Matti Hochorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoLucille Delisle avatar Lucille Delisleorcid logoClea Siguret avatar Clea Siguretorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoMo Heydarian avatar Mo HeydarianEkaterina Polkh avatar Ekaterina Polkhorcid logoMorgan Howells avatar Morgan Howellsorcid logoBérénice Batut avatar Bérénice Batutorcid logoMateo Boudet avatar Mateo BoudetHarriet Dashnow avatar Harriet Dashnoworcid logoFlorian Heyl avatar Florian Heylorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoCristóbal Gallardo avatar Cristóbal GallardoSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoMarisa Loach avatar Marisa Loach

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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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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de.NBI
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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.