animalcules: interactive microbiome analytics and visualization in R

Microbiome

Daniel Segrè¹  Yue Zhao²  Anthony Federico²  Tyler Faits²  Stefano Monti²  W. Evan Johnson³  Solaiappan Manimaran⁴ 

[1] Bioinformatics Program, College of Engineering, Boston University, Boston, MA, USA;Departments of Biology, Biomedical Engineering, and Physics, Boston University, Boston, MA, USA;Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA;Bioinformatics Program, College of Engineering, Boston University, Boston, MA, USA;Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA;Bioinformatics Program, College of Engineering, Boston University, Boston, MA, USA;Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA;Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA;Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA;

关键词: Microbiome analysis;    Visualization;    Interactive toolkit;    Biomarker identification;   

DOI  :  10.1186/s40168-021-01013-0

来源: Springer

【 摘 要 】

BackgroundMicrobial 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.ResultsTo 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.ConclusionsWe 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.C6TN5sLkpWMyzjfpfLhNCdVideo abstract

【 授权许可】

CC BY