ArticlePlant methods2020
DiCoExpress: a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models.
Article in Plant methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
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- The GT1 domain of RNase J ensures RNA quality control through dsRNA binding in Arabidopsis plastids.Nucleic acids research · 2026Article
- Suboptimal pre-anthesis water status mitigates wheat susceptibility to fusarium head blight and triggers specific metabolic responses.Scientific reports · 2025Article
- Expanding the clinicopathologic spectrum and genomic landscape of tumors with SMARCA2/4::CREM fusions.The Journal of pathology · 2024Article
- Transcriptomic changes in the PacC transcription factor deletion mutant of the plant pathogenic fungus Botrytis cinerea under acidic and neutral conditions.BMC genomic data · 2024Article
- Harbinger transposon insertion in ethylene signaling gene leads to emergence of new sexual forms in cucurbits.Nature communications · 2024Article
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- Highly resolved genome assembly and comparative transcriptome profiling reveal genes related to developmental stages of tapewormProceedings. Biological sciences · 2024Article
- Transcriptome and small RNAome profiling uncovers how a recombinant begomovirus evades RDRγ-mediated silencing of viral genes and outcompetes its parental virus in mixed infection.PLoS pathogens · 2024Article
- A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation.iScience · 2023Article
- Hierarchical contribution of individual lifestyle factors and their interactions on adenomatous and serrated polyp risk.Journal of gastroenterology · 2023Article
- Comparative phylotranscriptomics reveals ancestral and derived root nodule symbiosis programmes.Nature plants · 2023Article
- Localized osmotic stress activates systemic responses to N limitation inFrontiers in plant science · 2023Article
- The lipidome of an omnivorous insect responds to diet composition and social environment.Ecology and evolution · 2022Article
- Inheritance of Secondary Metabolites and Gene Expression Related to Tomato Fruit Quality.International journal of molecular sciences · 2022Article
- Article
- A Risk-Assessing Signature Based on Hypoxia- and Immune-Related Genes for Prognosis of Lung Adenocarcinoma Patients.Computational and mathematical methods in medicine · 2022Article
- Analysis of the Plant Mitochondrial Transcriptome.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Strive or thrive: Trends inFrontiers in plant science · 2022Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundRNAseq is nowadays the method of choice for transcriptome analysis. In the last decades, a high number of statistical methods, and associated bioinformatics tools, for RNAseq analysis were developed. More recently, statistical studies realised neutral comparison studies using benchmark datasets, shedding light on the most appropriate approaches for RNAseq data analysis.
resultsDiCoExpress is a script-based tool implemented in R that includes methods chosen based on their performance in neutral comparisons studies. DiCoExpress uses pre-existing R packages including FactoMineR, edgeR and coseq, to perform quality control, differential, and co-expression analysis of RNAseq data. Users can perform the full analysis, providing a mapped read expression data file and a file containing the information on the experimental design. Following the quality control step, the user can move on to the differential expression analysis performed using generalized linear models thanks to the automated contrast writing function. A co-expression analysis is implemented using the coseq package. Lists of differentially expressed genes and identified co-expression clusters are automatically analyzed for enrichment of annotations provided by the user. We used DiCoExpress to analyze a publicly available RNAseq dataset on the transcriptional response of
conclusionsDiCoExpress is an R script-based tool allowing users to perform a full RNAseq analysis from quality controls to co-expression analysis through differential analysis based on contrasts inside generalized linear models. DiCoExpress focuses on the statistical modelling of gene expression according to the experimental design and facilitates the data analysis leading the biological interpretation of the results.
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