ArticleNAR genomics and bioinformatics2020
dearseq: a variance component score test for RNA-seq differential analysis that effectively controls the false discovery rate.
Article in NAR genomics and bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- SIEVEseq: unified differential expression, variability, and skewness analyses using RNA-Seq data.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Gene set analysis for time-to-event outcome: comparison of a new approach based on the generalized Berk-Jones statistic with existing methods in presence of intra gene-set correlation.Briefings in bioinformatics · 2026Article
- Self-collected finger-prick blood for gene expression profiling: Unveiling early immune responses in mild COVID-19.iScience · 2026Article
- Impact of data compositionality on the detection of microbiota responses.Gut microbes · 2025Article
- AI-Enhanced Transcriptomic Discovery of Druggable Targets and Repurposed Therapies for Huntington's Disease.Brain sciences · 2025Review
- Article
- Neglecting the impact of normalization in semi-synthetic RNA-seq data simulations generates artificial false positives.Genome biology · 2024Article
- Article
- A vaccine targeting antigen-presenting cells through CD40 induces protective immunity against Nipah disease.Cell reports. Medicine · 2024Article
- Blood-based Transcriptomic and Proteomic Biomarkers of Emphysema.American journal of respiratory and critical care medicine · 2024Article
- Historical perspective and future directions: computational science in immuno-oncology.Journal for immunotherapy of cancer · 2024Review
- Article
- Neutrophil Activation and Immune Thrombosis Profiles Persist in Convalescent COVID-19.Journal of clinical immunology · 2023Article
- Genome-wide association study of a semicontinuous trait: illustration of the impact of the modeling strategy through the study of Neutrophil Extracellular Traps levels.NAR genomics and bioinformatics · 2023Article
- Kimma: flexible linear mixed effects modeling with kinship covariance for RNA-seq data.Bioinformatics (Oxford, England) · 2023Article
- benchdamic: benchmarking of differential abundance methods for microbiome data.Bioinformatics (Oxford, England) · 2023Article
- Exaggerated false positives by popular differential expression methods when analyzing human population samples.Genome biology · 2022Article
- CD177, a specific marker of neutrophil activation, is associated with coronavirus disease 2019 severity and death.iScience · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-seq studies are growing in size and popularity. We provide evidence that the most commonly used methods for differential expression analysis (DEA) may yield too many false positive results in some situations. We present dearseq, a new method for DEA that controls the false discovery rate (FDR) without making any assumption about the true distribution of RNA-seq data. We show that dearseq controls the FDR while maintaining strong statistical power compared to the most popular methods. We demonstrate this behavior with mathematical proofs, simulations and a real data set from a study of tuberculosis, where our method produces fewer apparent false positives.
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Registered trials
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