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 logoPeter van Heusden avatar Peter van Heusdenorcid logoCristóbal Gallardo avatar Cristóbal GallardoAndrea Bagnacani avatar Andrea Bagnacaniorcid logoMaria Doyle avatar Maria Doyleorcid logoNicola Soranzo avatar Nicola SoranzoDaniel Maticzka avatar Daniel MaticzkaPablo Moreno avatar Pablo Morenoorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoJulia Jakiela avatar Julia Jakielaorcid logoMarisa Loach avatar Marisa Loachorcid logoMateo Boudet avatar Mateo BoudetMarius van den Beek avatar Marius van den BeekCharlotte Adang avatar Charlotte Adangorcid logoMo Heydarian avatar Mo Heydarianorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoAnika Erxleben avatar Anika ErxlebenXi Liu avatar Xi LiuPeter-Bram 't Hoen avatar Peter-Bram 't HoenAnton Nekrutenko avatar Anton Nekrutenkoorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzThorben Stehling avatar Thorben StehlingHarriet Dashnow avatar Harriet DashnowNiall Beard avatar Niall Beardorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoBérénice Batut avatar Bérénice BatutOlivier Dameron avatar Olivier Dameronorcid logoToby Hodges avatar Toby HodgesEkaterina Polkh avatar Ekaterina PolkhAnne Siegel avatar Anne SiegelMarkus Wolfien avatar Markus Wolfienorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoSofoklis Keisaris avatar Sofoklis KeisarisMatt Ritchie avatar Matt RitchieJames Taylor avatar James Taylororcid logoArmin Dadras avatar Armin DadrasMehmet Tekman avatar Mehmet Tekmanorcid logoBjörn Grüning avatar Björn Grüningorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoClemens Blank avatar Clemens BlankIGC Bioinformatics Unit avatar IGC Bioinformatics UnitGildas Le Corguillé avatar Gildas Le Corguilléorcid logoHelena Rasche avatar Helena Rascheorcid logoMartin Čech avatar Martin Čechorcid logoWendi Bacon avatar Wendi BaconCasper de Visser avatar Casper de VisserXavier Garnier avatar Xavier Garnierorcid logoDiana Chiang Jurado avatar Diana Chiang JuradoSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoLinelle Abueg avatar Linelle Abuegorcid logoLucille Delisle avatar Lucille DelisleSimon Bray avatar Simon Brayorcid logoMorgan Howells avatar Morgan HowellsJovana Maksimovic avatar Jovana Maksimovicorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkMateusz Kuzak avatar Mateusz KuzakMatthias Bernt avatar Matthias Berntorcid logoErwan Corre avatar Erwan Correorcid logoGraeme Tyson avatar Graeme Tysonorcid logoAnne Fouilloux avatar Anne FouillouxJosé Manuel Domínguez avatar José Manuel DomínguezChao Zhang avatar Chao Zhangorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMira Kuntz avatar Mira KuntzWilliam Durand avatar William Durandorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoFlorian Heyl avatar Florian Heylorcid logoClea Siguret avatar Clea Siguretorcid logoMatti Hoch avatar Matti HochCharity Law avatar Charity LawAnna Trigos avatar Anna Trigosorcid logoTeresa Müller avatar Teresa MüllerCarlos Chee Mendonça avatar Carlos Chee MendonçaShian Su avatar Shian SuBelinda Phipson avatar Belinda Phipsonorcid logoTristan Reynolds avatar Tristan Reynolds

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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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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Australian BioCommons
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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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The University of Melbourne
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Melbourne Bioinformatics