Kandlikar Gaurav S, Gold Zachary J, Cowen Madeline C, Meyer Rachel S, Freise Amanda C, Kraft Nathan J B, Moberg-Parker Jordan, Sprague Joshua, Kushner David J, Curd Emily E
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Department of Microbiology and Microbial Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
F1000Res. 2018 Nov 1;7:1734. doi: 10.12688/f1000research.16680.1. eCollection 2018.
Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results.
环境DNA（eDNA）宏条形码分析正成为生态学和保护生物学的核心工具，并被越来越多地应用于教育、生物多样性监测以及公众宣传项目中，在这些项目里专业研究科学家会让社区合作伙伴参与到基础研究中。eDNA分析的结果能够吸引并教育自然资源管理者、学生、社区科学家和博物学家，但是如果没有生物信息学方面的大量培训，对于这个多样化的受众群体来说，与eDNA结果进行交互可能会很困难。在这里，我们展示了R包ranacapa，其核心是一个Shiny网络应用程序，可帮助进行探索性生物多样性分析和eDNA结果的可视化。该应用程序需要一个按样本分类的矩阵和一个包含每个样本描述性信息的简单元数据文件。该应用程序使用户能够通过交互式图形探索数据，并展示简单群落生态学分析的结果。我们向两组参与eDNA宏条形码分析结果的社区合作伙伴展示了ranacapa的价值。
