ImpulseDE: detection of differentially expressed genes in time series data using impulse models
ImpulseDE: detection of differentially expressed genes in time series data using impulse models
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DOI：
10.1093/bioinformatics/btw665
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发表时间：
2017-03-01
期刊：
影响因子：
5.8
通讯作者：
Yosef, Nir
中科院分区：
文献类型：
--
作者：
Sander, Jil;Schultze, Joachim L.;Yosef, Nir
环境的扰动会导致细胞内独特的基因表达变化。随着时间的推移，观察到这些变化可以表现为单一的脉冲式进展模式。ImPulseDE是一个R包，适合在高通量时间序列数据集中捕获这些模式。通过对每个基因拟合一个有代表性的脉冲模型，它报告了来自单个或两个实验的两个时间进程的时间点上差异表达的基因。为了优化运行时间，代码使用了集群和多线程。通过应用ImPulseDE，我们展示了它在微阵列和RNASeq数据中表示基因表达的潜在生物学的能力。可用性和实现：ImPulseDE可在BioConductor(https://bioconductor.)上获得Org/Packages/ImPulseDE/)。联系：niryosef@berkeley.edu.补充信息：补充数据可在BioInformation Online上获得。
Perturbations in the environment lead to distinctive gene expression changes within a cell. Observed over time, those variations can be characterized by single impulse-like progression patterns. ImpulseDE is an R package suited to capture these patterns in high throughput time series datasets. By fitting a representative impulse model to each gene, it reports differentially expressed genes across time points from a single or between two time courses from two experiments. To optimize running time, the code uses clustering and multi-threading. By applying ImpulseDE, we demonstrate its power to represent underlying biology of gene expression in microarray and RNA-Seq data.Availability and Implementation: ImpulseDE is available on Bioconductor (https://bioconductor. org/packages/ImpulseDE/).Contact: niryosef@berkeley.eduSupplementary information: Supplementary data are available at Bioinformatics online.