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
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
Pseudobulk Analysis with Decoupler and EdgeR
transcriptomics pseudobulk

Transcriptomics

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Transcriptomics
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
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
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

Contributors

This material was contributed to by:

Chao Zhang avatar Chao ZhangEkaterina Polkh avatar Ekaterina PolkhJosé Manuel Domínguez avatar José Manuel DomínguezAnton Nekrutenko avatar Anton NekrutenkoAndrea Bagnacani avatar Andrea Bagnacaniorcid logoLucille Delisle avatar Lucille Delisleorcid logoFlorian Heyl avatar Florian Heylorcid logoToby Hodges avatar Toby HodgesMateusz Kuzak avatar Mateusz Kuzakorcid logoNicola Soranzo avatar Nicola SoranzoAnne Siegel avatar Anne SiegelCharity Law avatar Charity LawCharlotte Adang avatar Charlotte Adangorcid logoMarisa Loach avatar Marisa Loachorcid logoClemens Blank avatar Clemens Blankorcid logoSofoklis Keisaris avatar Sofoklis KeisarisThorben Stehling avatar Thorben Stehlingorcid logoMatti Hoch avatar Matti HochPablo Moreno avatar Pablo Morenoorcid logoSaskia Hiltemann avatar Saskia HiltemannXi Liu avatar Xi Liuorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosMatt Ritchie avatar Matt Ritchieorcid logoMarius van den Beek avatar Marius van den Beekorcid logoMo Heydarian avatar Mo Heydarianorcid logoGraeme Tyson avatar Graeme TysonJames Taylor avatar James Taylororcid logoMateo Boudet avatar Mateo BoudetIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoMorgan Howells avatar Morgan HowellsDaniel Maticzka avatar Daniel MaticzkaOlivier Dameron avatar Olivier DameronMehmet Tekman avatar Mehmet Tekmanorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMira Kuntz avatar Mira KuntzJovana Maksimovic avatar Jovana Maksimovicorcid logoTeresa Müller avatar Teresa Müllerorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiXavier Garnier avatar Xavier Garnierorcid logoErwan Corre avatar Erwan Correorcid logoHelena Rasche avatar Helena Rascheorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoAnne Fouilloux avatar Anne FouillouxWilliam Durand avatar William DurandGildas Le Corguillé avatar Gildas Le CorguilléMarkus Wolfien avatar Markus Wolfienorcid logoBjörn Grüning avatar Björn GrüningAnna Trigos avatar Anna Trigosorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoArmin Dadras avatar Armin DadrasSimon Bray avatar Simon BraySanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoMaria Doyle avatar Maria Doyleorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoLinelle Abueg avatar Linelle AbuegCasper de Visser avatar Casper de Visserorcid logoClea Siguret avatar Clea SiguretHarriet Dashnow avatar Harriet Dashnoworcid logoBérénice Batut avatar Bérénice BatutBelinda Phipson avatar Belinda Phipsonorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoPeter van Heusden avatar Peter van HeusdenNiall Beard avatar Niall Beardorcid logoTristan Reynolds avatar Tristan ReynoldsShian Su avatar Shian Suorcid logoMartin Čech avatar Martin Čechorcid logoMatthias Bernt avatar Matthias Berntorcid logoJulia Jakiela avatar Julia JakielaCarlos Chee Mendonça avatar Carlos Chee Mendonçaorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoWendi Bacon avatar Wendi Baconorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDiana Chiang Jurado avatar Diana Chiang JuradoPeter-Bram 't Hoen avatar Peter-Bram 't Hoen

Funding

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

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Melbourne Bioinformatics
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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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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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The University of Melbourne
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Australian BioCommons
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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)