ArticleGenome biology2017
stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers, 3 of them syntheses that pooled it.
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Who cites it
79 citing papers in PubMed, 3 syntheses or guidelines pooled it.
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- Sex-specific DNA methylation differences in Alzheimer's disease pathology.Acta neuropathologica communications · 2021Pooled it
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- Ontogenetic Sequence of Differential Gene Expression in Predator-Induced Daphnia pulex.Molecular ecology · 2026Article
- Gene Expression and Alternative Splicing Throughout the Reproductive Cycle of a Viviparous Lizard Reveal Novel Genes for Pregnancy and Convergence With Squamates and Mammals.Molecular ecology · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
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- Multi-platform profiling reveals host- and cell -type-specific pseudorabies virus gene expression.Scientific reports · 2026Article
- Extending differential gene expression testing to handle genome aneuploidy in cancer.PLoS computational biology · 2026Article
- saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval.Genome biology · 2026Article
- Feeding-regulated glycogen metabolism drives rhythmic liver protein secretion.Nature metabolism · 2026Article
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- A whole-transcriptome analysis of differentially expressed genes, transcripts, and transcript usage in blood samples from Parkinson's disease patients.Experimental biology and medicine (Maywood, N.J.) · 2026Article
- isoespy: an integrated long-read transcriptome workflow for isoform resolution and visualization.Bioinformatics advances · 2026Article
- Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean.Nature communications · 2025Article
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- Oncogenic DEAD-box ATPase DDX41 establishes transcript ensembles via CLK3-dependent and -independent mechanisms.Nature communications · 2025Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA sequencing studies with complex designs and transcript-resolution analyses involve multiple hypotheses per gene; however, conventional approaches fail to control the false discovery rate (FDR) at gene level. We propose stageR, a two-stage testing paradigm that leverages the increased power of aggregated gene-level tests and allows post hoc assessment for significant genes. This method provides gene-level FDR control and boosts power for testing interaction effects. In transcript-level analysis, it provides a framework that performs powerful gene-level tests while maintaining biological interpretation at transcript-level resolution. The procedure is applicable whenever individual hypotheses can be aggregated, providing a unified framework for complex high-throughput experiments.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.