4.8 Article

animalcules: interactive microbiome analytics and visualization in R

期刊

MICROBIOME
卷 9, 期 1, 页码 -

出版社

BMC
DOI: 10.1186/s40168-021-01013-0

关键词

Microbiome analysis; Visualization; Interactive toolkit; Biomarker identification

资金

  1. NIH [R01GM127430, U01CA220413]
  2. Evans Center for Interdisciplinary Biomedical Research at the Boston University School of Medicine through the Affinity Research Collaborative on Systems Biology Approaches to Microbiome Research

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Animalcules is an interactive microbiome analysis toolkit that supports various types of microbiome data analysis, including 16S rRNA sequencing data, shotgun DNA metagenomics data, and RNA-sequencing based metatranscriptomics datasets. It combines traditional and novel analytics, visualization methods, and provides rich analysis features, allowing users to explore and discover insights from their data through command-line functions or an interactive interface.
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, 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. 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.

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