flexiMAP：一种基于回归的方法，用于在标准 RNA-seq 数据中发现差异的可变多聚腺苷酸化事件。
flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data.
机构信息
Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London WC1E 7HX, UK.
Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
出版信息
Bioinformatics. 2021 Jun 16;37(10):1461-1464. doi: 10.1093/bioinformatics/btaa854.
MOTIVATION
We present flexible Modeling of Alternative PolyAdenylation (flexiMAP), a new beta-regression-based method implemented in R, for discovering differential alternative polyadenylation events in standard RNA-seq data.
RESULTS
We show, using both simulated and real data, that flexiMAP exhibits a good balance between specificity and sensitivity and compares favourably to existing methods, especially at low fold changes. In addition, the tests on simulated data reveal some hitherto unrecognized caveats of existing methods. Importantly, flexiMAP allows modeling of multiple known covariates that often confound the results of RNA-seq data analysis.
AVAILABILITY AND IMPLEMENTATION
The flexiMAP R package is available at: https://github.com/kszkop/flexiMAP. Scripts and data to reproduce the analysis in this paper are available at: https://doi.org/10.5281/zenodo.3689788.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
我们提出了一种新的基于β回归的方法——灵活的可变 PolyA 分析（flexiMAP），它是在 R 中实现的，用于在标准 RNA-seq 数据中发现差异可变 PolyA 事件。
结果
我们使用模拟数据和真实数据表明，flexiMAP 在特异性和灵敏度之间表现出良好的平衡，并与现有的方法相比具有优势，特别是在低倍数变化时。此外，对模拟数据的测试揭示了现有方法迄今未被认识到的一些缺陷。重要的是，flexiMAP 允许对经常混淆 RNA-seq 数据分析结果的多个已知协变量进行建模。
可用性和实现
flexiMAP R 包可在：https://github.com/kszkop/flexiMAP 获得。本文分析的脚本和数据可在：https://doi.org/10.5281/zenodo.3689788 获得。
补充信息
补充数据可在生物信息学在线获得。
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