animalcules: interactive microbiome analytics and visualization in R.
animalcules: interactive microbiome analytics and visualization in R.
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DOI：
10.1186/s40168-021-01013-0
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发表时间：
2021-03-28
期刊：
影响因子：
15.5
通讯作者：
Johnson WE
中科院分区：
文献类型：
--
作者：
Zhao Y;Federico A;Faits T;Manimaran S;Segrè D;Monti S;Johnson WE
生活在人体内和体表的微生物群落对健康和疾病起着至关重要的作用。测序技术的最新进展使微生物群落的研究达到了前所未有的分辨率。然而，这些数据生成的进步给试图分析和可视化这些数据的研究人员带来了新的挑战。为了解决这些挑战，我们开发了animalcules，这是一个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、散弹枪DNA宏基因组学数据和基于rna的宏转录组学分析数据。该工具包结合了新颖和现有的分析、可视化方法和机器学习模型。例如，该工具包具有传统的微生物组分析，如α / β多样性和差异丰度分析，并结合了生物标志物鉴定的新方法。此外，animalcules还提供交互式和动态的图形，使用户能够理解他们的数据并发现新的见解。animalcules可以作为一个独立的命令行R包使用，或者用户可以使用附带的交互式R Shiny界面来探索他们的数据。我们介绍了animalcules，这是一个通过R Shiny提供的交互界面或各种命令行函数进行交互式微生物组分析的R包。它是第一个支持所有16S rRNA、基于dna的霰弹枪宏基因组学和基于rna测序的宏基因组学数据集分析的微生物组分析工具包。animalcules可以从GitHub （https://github.com/compbiomed/animalcules）免费下载，也可以通过Bioconductor （https://www.bioconductor.org/packages/release/bioc/html/animalcules.html）安装。视频摘要在线版本包含补充材料，可在10.1186/s40168-021-01013-0获得。
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. 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, the toolkit features traditional microbiome analyses such as alpha/beta diversity and differential abundance analysis, combined with new methods for biomarker identification are. In addition, animalcules provides interactive and dynamic figures that 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. 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. Video abstract The online version contains supplementary material available at 10.1186/s40168-021-01013-0.
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DOI：
10.1016/j.cgh.2018.09.017
发表时间：
2019-01
期刊：
Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association
影响因子：
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影响因子：
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通讯作者：
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