Background: Microbial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled the study of microbial communities at unprecedented resolution. However, these advances in data generation have presented novel challenges to researchers attempting to analyze and visualize these data. Results: To address some of these challenges, we have developed animalcules, an easy-to-use interactive microbiome analysis toolkit for 16S rRNA sequencing data, shotgun DNA metagenomics data, and RNA-based metatranscriptomics profiling data. This toolkit combines novel and existing analytics, visualization methods, and machine learning models. For example, traditional microbiome analyses such as alpha/beta diversity and differential abundance analysis are enhanced in the toolkit, while new methods such as biomarker identification are introduced. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data and discover new insights. animalcules can be used as a standalone command-line R package or users can explore their data with the accompanying interactive R Shiny interface. Conclusions: We present animalcules, an R package for interactive microbiome analysis through either an interactive interface facilitated by R Shiny or various command-line functions. It is the first microbiome analysis toolkit that supports the analysis of all 16S rRNA, DNA-based shotgun metagenomics, and RNA-sequencing based metatranscriptomics datasets. animalcules can be freely downloaded from GitHub at https://github.com/compbiomed/animalcules or installed through Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/animalcules.html.

中文翻译：

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动物：交互式微生物组分析1和R中的可视化

背景：生活在人体中和人体上的微生物群落在健康和疾病中起着至关重要的作用。测序技术的最新进展使人们能够以前所未有的分辨率研究微生物群落。但是，数据生成的这些进步给试图分析和可视化这些数据的研究人员提出了新的挑战。结果：为了解决其中的一些挑战，我们开发了Animalcules，这是一种易于使用的交互式微生物组分析工具包，用于16S rRNA测序数据，shot弹枪DNA宏基因组学数据和基于RNA的元转录组学分析数据。该工具包结合了新颖和现有的分析，可视化方法以及机器学习模型。例如，该工具包中增强了传统的微生物组分析，例如alpha / beta多样性和差异丰度分析，同时引入了诸如生物标记识别的新方法。动物产生的强大的互动和动态图形使用户能够理解他们的数据并发现新的见解。可以将animalcules用作独立的命令行R包，或者用户可以使用随附的交互式R Shiny界面浏览其数据。结论：我们介绍了Animalcules，这是一个R包，用于通过R Shiny促进的交互式界面或各种命令行功能进行交互式微生物组分析。它是第一个支持所有16S rRNA，基于DNA的shot弹枪宏基因组学和基于RNA测序的元转录组学数据集分析的微生物组分析工具包。您可以从GitHub上的https://github.com/compbiomed/animalcules上免费下载animalcules，也可以通过Bioconductor在https：// www上进行安装。