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:

Anna Trigos avatar Anna Trigosorcid logoToby Hodges avatar Toby HodgesMatt Ritchie avatar Matt Ritchieorcid logoBjörn Grüning avatar Björn Grüningorcid logoFlorian Heyl avatar Florian Heylorcid logoMorgan Howells avatar Morgan HowellsEkaterina Polkh avatar Ekaterina Polkhorcid logoMartin Čech avatar Martin Čechorcid logoMo Heydarian avatar Mo Heydarianorcid logoMarius van den Beek avatar Marius van den Beekorcid logoClea Siguret avatar Clea Siguretorcid logoErwan Corre avatar Erwan Correorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoCristóbal Gallardo avatar Cristóbal GallardoCharity Law avatar Charity LawAnton Nekrutenko avatar Anton NekrutenkoPeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoBérénice Batut avatar Bérénice Batutorcid logoMallory Freeberg avatar Mallory FreebergGildas Le Corguillé avatar Gildas Le CorguilléCasper de Visser avatar Casper de VisserCharlotte Adang avatar Charlotte AdangIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoHelena Rasche avatar Helena Rascheorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoMatti Hoch avatar Matti Hochorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoMateo Boudet avatar Mateo Boudetorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoArmin Dadras avatar Armin DadrasSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzMateusz Kuzak avatar Mateusz KuzakOlivier Dameron avatar Olivier DameronPablo Moreno avatar Pablo Morenoorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosHarriet Dashnow avatar Harriet DashnowNiall Beard avatar Niall Beardorcid logoWendi Bacon avatar Wendi Baconorcid logoMarisa Loach avatar Marisa LoachJovana Maksimovic avatar Jovana Maksimovicorcid logoJulia Jakiela avatar Julia JakielaXi Liu avatar Xi Liuorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoAnika Erxleben avatar Anika ErxlebenAnne Siegel avatar Anne Siegelorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoMarkus Wolfien avatar Markus Wolfienorcid logoMyrthe van Baardwijk avatar Myrthe van BaardwijkDaniel Maticzka avatar Daniel MaticzkaXavier Garnier avatar Xavier Garnierorcid logoMatthias Bernt avatar Matthias Berntorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoGraeme Tyson avatar Graeme Tysonorcid logoLucille Delisle avatar Lucille Delisleorcid logoTeresa Müller avatar Teresa Müllerorcid logoNicola Soranzo avatar Nicola SoranzoChao Zhang avatar Chao Zhangorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoClemens Blank avatar Clemens BlankJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoTristan Reynolds avatar Tristan ReynoldsShian Su avatar Shian SuSimon Bray avatar Simon BrayBelinda Phipson avatar Belinda PhipsonThorben Stehling avatar Thorben StehlingWilliam Durand avatar William DurandMehmet Tekman avatar Mehmet Tekmanorcid logoDiana Chiang Jurado avatar Diana Chiang JuradoJames Taylor avatar James TaylorAndrea Bagnacani avatar Andrea Bagnacaniorcid logoMira Kuntz avatar Mira Kuntzorcid logoLinelle Abueg avatar Linelle AbuegCarlos Chee Mendonça avatar Carlos Chee Mendonçaorcid logoMaria Doyle avatar Maria Doyle

Funding

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

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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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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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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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Melbourne Bioinformatics
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de.NBI