mirrorCheck: an R package facilitating informed use of DESeq2's lfcShrink() function for differential gene expression analysis of clinical samples.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Bioinformatics advances Pub Date : 2025-04-02 eCollection Date: 2025-01-01 DOI:10.1093/bioadv/vbaf070

Katherine Elise Scull, Kiarash Behrouzfar, Daniella Brasacchio, Enid Yi Ni Lam, Dineika Chandrananda, Paul Yeh

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引用次数: 0

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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mirrorCheck：一个R包，方便使用DESeq2的lfcShrink（）函数对临床样本进行差异基因表达分析。

动机：在DESeq2包中实现的用于差异基因表达分析的复杂lfcShrink（）函数旨在减少大量rna测序数据中低读取计数和/或高可变基因的噪声，从而避免了任意过滤阈值的需要。然而，在分析具有多种生物学相关分组的临床数据时，可能会出现困难。特别是，改变参照组可以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，我们提出了mirrorCheck，这是一个R包，用于自动化有条理的lfcShrink（）使用和数据可视化，以便在分析过程中进行质量控制和数据驱动决策。可用性和实现：源代码，包括文档，可在github上获得https://github.com/kescull/mirrorCheck。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Bioinformatics advances

CiteScore

1.60

自引率

0.00%

发文量