ArticleBioinformatics advances2025
mirrorCheck: an R package facilitating informed use of DESeq2's lfcShrink() function for differential gene expression analysis of clinical samples.
Article in Bioinformatics advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
2 citing papers in PubMed.
- IGFBP3 repression driven by inflammation links air pollution to placental and developmental defects.EMBO molecular medicine · 2026Article
- miR-142-5p promotes TSCM differentiation and suppresses progressive T-cell maturation via targeting PRKCB.Frontiers in immunology · 2026Article
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Authors and funding
6 authors.
Funding
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Abstract
Motivation: The sophisticated lfcShrink() function implemented in the DESeq2 package for differential gene expression analysis aims to reduce noise from low read count and/or highly variable genes in bulk RNA-sequencing data, thus circumventing the need for arbitrary filtering thresholds. However, difficulties can arise when analysing clinical data with multiple biologically-relevant groupings. In particular, changing the reference group can dramatically alter the ranking of differentially expressed genes, instead of merely 'mirroring' the up- and down-regulated genes in reciprocal comparisons. Results: Here, we present mirrorCheck, an R package to automate methodical lfcShrink() usage and data visualization for quality control and data-driven decision-making during analysis. Availability and implementation: The source code, including documentation, is available on github at https://github.com/kescull/mirrorCheck.
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Registered trials
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.