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:

orcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzSimon Bray avatar Simon Brayorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMira Kuntz avatar Mira Kuntzorcid logoArmin Dadras avatar Armin DadrasPeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoToby Hodges avatar Toby HodgesEkaterina Polkh avatar Ekaterina Polkhorcid logoTristan Reynolds avatar Tristan ReynoldsCasper de Visser avatar Casper de Visserorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoTeresa Müller avatar Teresa Müllerorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoMarisa Loach avatar Marisa LoachMarkus Wolfien avatar Markus WolfienCharity Law avatar Charity LawThorben Stehling avatar Thorben StehlingNiall Beard avatar Niall Beardorcid logoAnthony Bretaudeau avatar Anthony BretaudeauShian Su avatar Shian SuMatt Ritchie avatar Matt RitchieXavier Garnier avatar Xavier Garnierorcid logoWendi Bacon avatar Wendi Baconorcid logoErwan Corre avatar Erwan Correorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoMateo Boudet avatar Mateo BoudetOlivier Dameron avatar Olivier Dameronorcid logoMatthias Bernt avatar Matthias BerntSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkGildas Le Corguillé avatar Gildas Le CorguilléIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoFlorian Heyl avatar Florian Heylorcid logoMartin Čech avatar Martin Čechorcid logoMatti Hoch avatar Matti HochMehmet Tekman avatar Mehmet TekmanCharlotte Adang avatar Charlotte AdangMateusz Kuzak avatar Mateusz KuzakChao Zhang avatar Chao Zhangorcid logoBérénice Batut avatar Bérénice Batutorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoLinelle Abueg avatar Linelle Abuegorcid logoHelena Rasche avatar Helena RascheHarriet Dashnow avatar Harriet DashnowAndrea Bagnacani avatar Andrea Bagnacaniorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoClemens Blank avatar Clemens Blankorcid logoMarius van den Beek avatar Marius van den BeekJovana Maksimovic avatar Jovana MaksimovicWilliam Durand avatar William Durandorcid logoMaria Doyle avatar Maria Doyleorcid logoNicola Soranzo avatar Nicola SoranzoDaniel Maticzka avatar Daniel Maticzkaorcid logoBjörn Grüning avatar Björn GrüningBelinda Phipson avatar Belinda Phipsonorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoClea Siguret avatar Clea Siguretorcid logoSaskia Hiltemann avatar Saskia HiltemannAnton Nekrutenko avatar Anton Nekrutenkoorcid logoLucille Delisle avatar Lucille Delisleorcid logoJulia Jakiela avatar Julia JakielaAnne Siegel avatar Anne Siegelorcid logoMorgan Howells avatar Morgan HowellsJames Taylor avatar James TaylorXi Liu avatar Xi Liuorcid logoWolfgang Maier avatar Wolfgang MaierAnna Trigos avatar Anna Trigosorcid logoGraeme Tyson avatar Graeme Tysonorcid logoMo Heydarian avatar Mo HeydarianCarlos Chee Mendonça avatar Carlos Chee MendonçaPablo Moreno avatar Pablo Morenoorcid logoCristóbal Gallardo avatar Cristóbal Gallardo

Funding

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

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de.NBI
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The University of Melbourne
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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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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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Australian BioCommons