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 logoClea Siguret avatar Clea Siguretorcid logoMorgan Howells avatar Morgan Howellsorcid logoPavankumar Videm avatar Pavankumar VidemXi Liu avatar Xi Liuorcid logoWendi Bacon avatar Wendi Baconorcid logoAnne Fouilloux avatar Anne FouillouxAnna Trigos avatar Anna TrigosAnton Nekrutenko avatar Anton NekrutenkoCarlos Chee Mendonça avatar Carlos Chee Mendonçaorcid logoBérénice Batut avatar Bérénice Batutorcid logoMallory Freeberg avatar Mallory FreebergPablo Moreno avatar Pablo Morenoorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiJames Taylor avatar James TaylorMehmet Tekman avatar Mehmet TekmanSimon Bray avatar Simon Brayorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoJulia Jakiela avatar Julia JakielaCasper de Visser avatar Casper de VisserHarriet Dashnow avatar Harriet Dashnoworcid logoLucille Delisle avatar Lucille DelisleJovana Maksimovic avatar Jovana MaksimovicGildas Le Corguillé avatar Gildas Le Corguilléorcid logoMarisa Loach avatar Marisa Loachorcid logoMartin Čech avatar Martin Čechorcid logoMarius van den Beek avatar Marius van den Beekorcid logoToby Hodges avatar Toby Hodgesorcid logoErwan Corre avatar Erwan CorreCharity Law avatar Charity Laworcid logoMaria Doyle avatar Maria DoylePeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoMarek Ostaszewski avatar Marek OstaszewskiNiall Beard avatar Niall Beardorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoBjörn Grüning avatar Björn Grüningorcid logoFlorian Heyl avatar Florian HeylEkaterina Polkh avatar Ekaterina PolkhJosé Manuel Domínguez avatar José Manuel DomínguezBelinda Phipson avatar Belinda Phipsonorcid logoAnika Erxleben avatar Anika ErxlebenThorben Stehling avatar Thorben Stehlingorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoHelena Rasche avatar Helena RascheCharlotte Adang avatar Charlotte AdangMatt Ritchie avatar Matt RitchieMateusz Kuzak avatar Mateusz Kuzakorcid logoGraeme Tyson avatar Graeme TysonAnne Siegel avatar Anne Siegelorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoMatti Hoch avatar Matti HochAndrea Bagnacani avatar Andrea Bagnacaniorcid logoMateo Boudet avatar Mateo BoudetShian Su avatar Shian SuXavier Garnier avatar Xavier GarnierDaniel Maticzka avatar Daniel Maticzkaorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoTeresa Müller avatar Teresa Müllerorcid logoMo Heydarian avatar Mo HeydarianMarkus Wolfien avatar Markus Wolfienorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoLinelle Abueg avatar Linelle Abuegorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoMira Kuntz avatar Mira Kuntzorcid logoArmin Dadras avatar Armin Dadrasorcid logoIacopo Cristoferi avatar Iacopo CristoferiIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoTristan Reynolds avatar Tristan ReynoldsOlivier Dameron avatar Olivier Dameronorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoMatthias Bernt avatar Matthias BerntChao Zhang avatar Chao Zhangorcid logoCristóbal Gallardo avatar Cristóbal GallardoWilliam Durand avatar William DurandSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoClemens Blank avatar Clemens Blank

Funding

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

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Australian BioCommons
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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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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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The University of Melbourne
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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.