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 logoMorgan Howells avatar Morgan HowellsDaniel Maticzka avatar Daniel Maticzkaorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkChao Zhang avatar Chao ZhangIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMateo Boudet avatar Mateo Boudetorcid logoSofoklis Keisaris avatar Sofoklis KeisarisNiall Beard avatar Niall BeardXi Liu avatar Xi LiuOlivier Dameron avatar Olivier Dameronorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoHelena Rasche avatar Helena Rascheorcid logoBjörn Grüning avatar Björn Grüningorcid logoMatthias Bernt avatar Matthias BerntCharity Law avatar Charity LawAnne Siegel avatar Anne Siegelorcid logoErwan Corre avatar Erwan Correorcid logoWendi Bacon avatar Wendi BaconJosé Manuel Domínguez avatar José Manuel DomínguezWilliam Durand avatar William Durandorcid logoLucille Delisle avatar Lucille DelisleAnna Trigos avatar Anna TrigosPablo Moreno avatar Pablo MorenoSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoMira Kuntz avatar Mira Kuntzorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoFlorian Heyl avatar Florian Heylorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoJulia Jakiela avatar Julia Jakielaorcid logoClemens Blank avatar Clemens BlankPeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoMatti Hoch avatar Matti Hochorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiMateusz Kuzak avatar Mateusz Kuzakorcid logoNicola Soranzo avatar Nicola SoranzoJames Taylor avatar James Taylororcid logoWolfgang Maier avatar Wolfgang Maierorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzCharlotte Adang avatar Charlotte Adangorcid logoMaria Doyle avatar Maria Doyleorcid logoLinelle Abueg avatar Linelle AbuegHarriet Dashnow avatar Harriet Dashnoworcid logoTeresa Müller avatar Teresa MüllerCarlos Chee Mendonça avatar Carlos Chee MendonçaCasper de Visser avatar Casper de Visserorcid logoClea Siguret avatar Clea Siguretorcid logoIacopo Cristoferi avatar Iacopo CristoferiMatt Ritchie avatar Matt Ritchieorcid logoMarius van den Beek avatar Marius van den Beekorcid logoSaskia Hiltemann avatar Saskia HiltemannBelinda Phipson avatar Belinda Phipsonorcid logoBérénice Batut avatar Bérénice Batutorcid logoToby Hodges avatar Toby HodgesMehmet Tekman avatar Mehmet TekmanAndrea Bagnacani avatar Andrea BagnacaniMarkus Wolfien avatar Markus Wolfienorcid logoGraeme Tyson avatar Graeme Tysonorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoMallory Freeberg avatar Mallory Freebergorcid logoMartin Čech avatar Martin ČechThorben Stehling avatar Thorben StehlingSimon Bray avatar Simon BrayEkaterina Polkh avatar Ekaterina PolkhGildas Le Corguillé avatar Gildas Le Corguilléorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoXavier Garnier avatar Xavier GarnierJovana Maksimovic avatar Jovana MaksimovicAnton Nekrutenko avatar Anton Nekrutenkoorcid logoArmin Dadras avatar Armin Dadrasorcid logoMarisa Loach avatar Marisa Loachorcid logoMo Heydarian avatar Mo HeydarianShian Su avatar Shian Suorcid 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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Melbourne Bioinformatics
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The University of Melbourne
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Australian BioCommons
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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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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)