Polyester: simulating RNA-seq datasets with differential transcript expression
Polyester: simulating RNA-seq datasets with differential transcript expression
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DOI：
10.1093/bioinformatics/btv272
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发表时间：
2015-09-01
期刊：
影响因子：
5.8
通讯作者：
Leek, Jeffrey T.
中科院分区：
文献类型：
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作者：
Frazee, Alyssa C.;Jaffe, Andrew E.;Leek, Jeffrey T.
动机：RNA 测序差异表达分析 (RNA-seq) 的统计方法开发需要软件工具来评估准确性和错误率控制。由于实验数据集中真正的差异表达状态通常是未知的，因此必须利用人工构建的数据集，要么通过生成昂贵的掺入实验，要么通过模拟 RNA-seq 数据。结果：Polyester 是一个 R 包，旨在模拟 RNA-seq 数据，从实验设计开始，以 RNA-seq 读数的集合结束。其主要优点是能够模拟读数，指示各种实验设计的生物重复中异构体水平的差异表达。 Polyester 生成的数据是真实 RNA-seq 数据的合理近似，标准差异表达工作流程可以恢复用户在模拟中设置的差异表达。
Motivation: Statistical methods development for differential expression analysis of RNA sequencing (RNA-seq) requires software tools to assess accuracy and error rate control. Since true differential expression status is often unknown in experimental datasets, artificially constructed datasets must be utilized, either by generating costly spike-in experiments or by simulating RNA-seq data.Results: Polyester is an R package designed to simulate RNA-seq data, beginning with an experimental design and ending with collections of RNA-seq reads. Its main advantage is the ability to simulate reads indicating isoform-level differential expression across biological replicates for a variety of experimental designs. Data generated by Polyester is a reasonable approximation to real RNA-seq data and standard differential expression workflows can recover differential expression set in the simulation by the user.