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StructuRly:一个新颖的 shiny 应用程序,用于生成全面、详细和交互式的群体遗传分析图。

StructuRly: A novel shiny app to produce comprehensive, detailed and interactive plots for population genetic analysis.

机构信息

Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland.

Istituto per le Applicazioni del Calcolo "M. Picone", National Research Council, Naples, Italy.

出版信息

PLoS One. 2020 Feb 19;15(2):e0229330. doi: 10.1371/journal.pone.0229330. eCollection 2020.

DOI:10.1371/journal.pone.0229330
PMID:32074134
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7029954/
Abstract

Population genetics focuses on the analysis of genetic differences within and between-group of individuals and the inference of the populations' structure. These analyses are usually carried out using Bayesian clustering or maximum likelihood estimation algorithms that assign individuals to a given population depending on specific genetic patterns. Although several tools were developed to perform population genetics analysis, their standard graphical outputs may not be sufficiently informative for users lacking interactivity and complete information. StructuRly aims to resolve this problem by offering a complete environment for population analysis. In particular, StructuRly combines the statistical power of the R language with the friendly interfaces implemented using the shiny libraries to provide a novel tool for performing population clustering, evaluating several genetic indexes, and comparing results. Moreover, graphical representations are interactive and can be easily personalized. StructuRly is available either as R package on GitHub, with detailed information for its installation and use and as shinyapps.io servers for those users who are not familiar with R and the RStudio IDE. The application has been tested on Linux, macOS and Windows operative systems and can be launched as a shiny app in every web browser.

摘要

群体遗传学专注于分析个体内部和个体之间的遗传差异,并推断群体的结构。这些分析通常使用贝叶斯聚类或最大似然估计算法来进行,根据特定的遗传模式将个体分配到给定的群体中。尽管已经开发了几种工具来进行群体遗传学分析,但它们的标准图形输出对于缺乏交互性和完整信息的用户来说可能不够直观。StructuRly 旨在通过提供一个完整的群体分析环境来解决这个问题。具体来说,StructuRly 将 R 语言的统计能力与使用 shiny 库实现的友好界面相结合,为执行群体聚类、评估几个遗传指标和比较结果提供了一个新的工具。此外,图形表示是交互式的,可以轻松地进行个性化设置。StructuRly 可以在 GitHub 上作为 R 包使用,其中包含了有关安装和使用的详细信息,也可以在 shinyapps.io 服务器上使用,对于那些不熟悉 R 和 RStudio IDE 的用户来说非常方便。该应用程序已经在 Linux、macOS 和 Windows 操作系统上进行了测试,可以在每个网络浏览器中作为 shiny 应用程序启动。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ba44/7029954/49946d0f2266/pone.0229330.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ba44/7029954/53e91d08470a/pone.0229330.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ba44/7029954/b506e88daf8d/pone.0229330.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ba44/7029954/643b31fe724d/pone.0229330.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ba44/7029954/f2d29581b630/pone.0229330.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ba44/7029954/49946d0f2266/pone.0229330.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ba44/7029954/53e91d08470a/pone.0229330.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ba44/7029954/b506e88daf8d/pone.0229330.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ba44/7029954/643b31fe724d/pone.0229330.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ba44/7029954/f2d29581b630/pone.0229330.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ba44/7029954/49946d0f2266/pone.0229330.g005.jpg

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