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 logoJulia Jakiela avatar Julia Jakielaorcid logoMarek Ostaszewski avatar Marek OstaszewskiMateusz Kuzak avatar Mateusz Kuzakorcid logoHelena Rasche avatar Helena Rascheorcid logoMarisa Loach avatar Marisa LoachXi Liu avatar Xi LiuEkaterina Polkh avatar Ekaterina Polkhorcid logoTeresa Müller avatar Teresa MüllerAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiThorben Stehling avatar Thorben Stehlingorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoBérénice Batut avatar Bérénice Batutorcid logoSofoklis Keisaris avatar Sofoklis KeisarisAndrea Bagnacani avatar Andrea Bagnacaniorcid logoLinelle Abueg avatar Linelle AbuegIGC Bioinformatics Unit avatar IGC Bioinformatics UnitJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoMaria Doyle avatar Maria Doyleorcid logoLucille Delisle avatar Lucille Delisleorcid logoClemens Blank avatar Clemens BlankOlivier Dameron avatar Olivier DameronWilliam Durand avatar William Durandorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoToby Hodges avatar Toby HodgesBelinda Phipson avatar Belinda PhipsonJames Taylor avatar James TaylorPablo Moreno avatar Pablo MorenoChao Zhang avatar Chao Zhangorcid logoPavankumar Videm avatar Pavankumar VidemPeter-Bram 't Hoen avatar Peter-Bram 't HoenNiall Beard avatar Niall Beardorcid logoMateo Boudet avatar Mateo BoudetXavier Garnier avatar Xavier Garnierorcid logoBjörn Grüning avatar Björn GrüningMarkus Wolfien avatar Markus Wolfienorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoMatthias Bernt avatar Matthias Berntorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzSimon Bray avatar Simon BrayAnne Siegel avatar Anne Siegelorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoGraeme Tyson avatar Graeme Tysonorcid logoMira Kuntz avatar Mira KuntzMatt Ritchie avatar Matt Ritchieorcid logoTristan Reynolds avatar Tristan ReynoldsGildas Le Corguillé avatar Gildas Le Corguilléorcid logoWendi Bacon avatar Wendi BaconMehmet Tekman avatar Mehmet TekmanDaniel Maticzka avatar Daniel Maticzkaorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoMallory Freeberg avatar Mallory FreebergCasper de Visser avatar Casper de Visserorcid logoClea Siguret avatar Clea SiguretCharity Law avatar Charity Laworcid logoAnika Erxleben avatar Anika Erxlebenorcid logoMo Heydarian avatar Mo Heydarianorcid logoMorgan Howells avatar Morgan HowellsHarriet Dashnow avatar Harriet Dashnoworcid logoFlorian Heyl avatar Florian HeylShian Su avatar Shian SuSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamCharlotte Adang avatar Charlotte Adangorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMatti Hoch avatar Matti Hochorcid logoSaskia Hiltemann avatar Saskia HiltemannCarlos Chee Mendonça avatar Carlos Chee Mendonçaorcid logoMartin Čech avatar Martin ČechAnna Trigos avatar Anna TrigosJovana Maksimovic avatar Jovana Maksimovicorcid logoErwan Corre avatar Erwan Correorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoMarius van den Beek avatar Marius van den Beekorcid logoArmin Dadras avatar Armin Dadrasorcid logoDiana Chiang Jurado avatar Diana Chiang Jurado

Funding

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

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Melbourne Bioinformatics
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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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Australian BioCommons
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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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The University of Melbourne
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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)