Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Accéder directement au contenu
Article Dans Une Revue Journal of visualized experiments : JoVE Année : 2022

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Résumé

Summary: DiCoExpress is a script-based tool implemented in R to perform an RNA-Seq analysis from quality control to co-expression. DiCoExpress handles complete and unbalanced design up to 2 biological factors. This video tutorial guides the user through the different features of DiCoExpress. Abstract: The proper use of statistical modeling in NGS data analysis requires an advanced level of expertise. There has recently been a growing consensus on using generalized linear models for differential analysis of RNA-Seq data and the advantage of mixture models to perform co-expression analysis. To offer a managed setting to use these modeling approaches, we developed DiCoExpress that provides a standardized R pipeline to perform an RNA-Seq analysis. Without any particular knowledge in statistics or R programming, beginners can perform a complete RNA-Seq analysis from quality controls to co-expression through differential analysis based on contrasts inside a generalized linear model. An enrichment analysis is proposed both on the lists of differentially expressed genes, and the co-expressed gene clusters. This video tutorial is conceived as a step-by-step protocol to help users take full advantage of DiCoExpress and its potential in empowering the biological interpretation of an RNA-Seq experiment.
Fichier non déposé

Dates et versions

hal-04274577 , version 1 (08-11-2023)

Identifiants

Citer

Kevin Baudry, Christine Paysant-Le Roux, Stefano Colella, Benoît Castandet, Marie-Laure Martin-Magniette. Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress. Journal of visualized experiments : JoVE, 2022, 185, pp.e62566. ⟨10.3791/62566⟩. ⟨hal-04274577⟩
233 Consultations
0 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More