mirrorCheck：一个R包，有助于在临床样本的差异基因表达分析中明智地使用DESeq2的lfcShrink()函数。
mirrorCheck: an R package facilitating informed use of DESeq2's lfcShrink() function for differential gene expression analysis of clinical samples.
作者信息
Scull Katherine Elise, Behrouzfar Kiarash, Brasacchio Daniella, Lam Enid Yi Ni, Chandrananda Dineika, Yeh Paul
机构信息
Blood Cancer Biomarkers Lab, Department of Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, 3168, Australia.
Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia.
出版信息
Bioinform Adv. 2025 Apr 2;5(1):vbaf070. doi: 10.1093/bioadv/vbaf070. eCollection 2025.
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.
动机
DESeq2软件包中实现的用于差异基因表达分析的复杂lfcShrink()函数旨在减少批量RNA测序数据中低读数计数和/或高变异性基因的噪声，从而避免了对任意过滤阈值的需求。然而，在分析具有多个生物学相关分组的临床数据时可能会出现困难。特别是，改变参考组会显著改变差异表达基因的排名，而不仅仅是在相互比较中“反映”上调和下调的基因。
结果
在这里，我们展示了mirrorCheck，这是一个R软件包，用于在分析过程中自动进行有条理的lfcShrink()使用和数据可视化，以进行质量控制和数据驱动的决策。
可用性和实现
包括文档在内的源代码可在github上获取，网址为https://github.com/kescull/mirrorCheck。
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