OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data.
OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data.
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DOI：
10.1093/bioinformatics/btw004
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发表时间：
2016-05-01
期刊：
影响因子：
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通讯作者：
Stewart R
中科院分区：
文献类型：
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作者：
Leng N;Choi J;Chu LF;Thomson JA;Kendziorski C;Stewart R
摘要：最近的一篇文章在Fluidigm C1平台生成的多个单细胞RNA-seq（scRNA-seq）数据集中发现了一个伪影。具体而言，Leng等人显示从具有小或大平板输出ID的位点捕获的细胞中的基因表达显著增加。我们将这种伪影称为排序效应（OE）。在下游分析中包括OE基因可能导致偏倚结果。为了解决这个问题，我们开发了一种名为OE的统计方法和软件来识别OE基因的排序列表。OEASIS作为R软件包沿着用户友好的图形界面实现，允许用户检查Fluidigm C1平台生成的scRNA-seq数据中的潜在伪影。可用性和实施：OEASYPE可在https://github.com/lengning/OEFinder上免费获得，联系方式：rstewart@morgridge.org或lengning1@gmail.com补充信息：补充数据可在生物信息学在线获得。
Summary: A recent article identified an artifact in multiple single-cell RNA-seq (scRNA-seq) datasets generated by the Fluidigm C1 platform. Specifically, Leng et al. showed significantly increased gene expression in cells captured from sites with small or large plate output IDs. We refer to this artifact as an ordering effect (OE). Including OE genes in downstream analyses could lead to biased results. To address this problem, we developed a statistical method and software called OEFinder to identify a sorted list of OE genes. OEFinder is available as an R package along with user-friendly graphical interface implementations which allows users to check for potential artifacts in scRNA-seq data generated by the Fluidigm C1 platform. Availability and implementation: OEFinder is freely available at https://github.com/lengning/OEFinder Contact: rstewart@morgridge.org or lengning1@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.