meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays
meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays
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DOI：
10.1371/journal.pcbi.1006506
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发表时间：
2018-10-01
影响因子：
4.3
通讯作者：
Eglen, Stephen J.
中科院分区：
文献类型：
--
作者：
Gelfman, Sahar;Wang, Quanli;Eglen, Stephen J.
在这里，我们提出了一个开源的R包“meaRtools”，它提供了一个平台，用于分析记录在微电极阵列（MEA）上的神经网络。用MEA监测的培养神经元网络现在被广泛用于表征神经系统疾病的体外模型和评价药物化合物。meaRtools提供核心算法，用于MEA尖峰序列分析、特征提取、统计分析和绘制具有多种基因型和治疗的多种MEA记录。meaRtools的功能涵盖了锋电位序列分析的新解决方案，包括使用锋电位序列平铺系数（STTC）、互信息、同步爆发和培养威尔斯孔内的熵来评估电极互相关的算法。还集成的是一个解决方案，以占突发的变异性起源于混合细胞的神经元培养。该软件包提供了一个专门为MEA数据构建的统计平台，可以联合收割机组合多个MEA记录，并比较不同遗传模型或治疗之间提取的特征。我们证明了利用meaRtools成功地识别出Celf4基因敲除小鼠神经元网络中的癫痫样表型。该软件包在GPL许可证（GPL> = 3）下免费提供，并在CRAN Web服务器存储库上频繁更新。该软件包以及完整的文档沿着可以从以下网站下载：https://cran.r-project.org/web/packages/meaRtools/。
Here we present an open-source R package 'meaRtools' that provides a platform for analyzing neuronal networks recorded on Microelectrode Arrays (MEAs). Cultured neuronal networks monitored with MEAs are now being widely used to characterize in vitro models of neurological disorders and to evaluate pharmaceutical compounds. meaRtools provides core algorithms for MEA spike train analysis, feature extraction, statistical analysis and plotting of multiple MEA recordings with multiple genotypes and treatments. meaRtools functionality covers novel solutions for spike train analysis, including algorithms to assess electrode cross-correlation using the spike train tiling coefficient (STTC), mutual information, synchronized bursts and entropy within cultured wells. Also integrated is a solution to account for bursts variability originating from mixed-cell neuronal cultures. The package provides a statistical platform built specifically for MEA data that can combine multiple MEA recordings and compare extracted features between different genetic models or treatments. We demonstrate the utilization of meaRtools to successfully identify epilepsy-like phenotypes in neuronal networks from Celf4 knockout mice. The package is freely available under the GPL license (GPL> = 3) and is updated frequently on the CRAN web-server repository. The package, along with full documentation can be downloaded from: https://cran.r-project.org/web/packages/meaRtools/.