ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; peer review: 1 approved, 2 approved with reservations]

• Published in: F1000 research Vol. 7; p. 1734
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: England Faculty of 1000 Ltd 2018; F1000 Research Limited; F1000 Research Ltd
• Subjects: Biodiversity; Bioinformatics; Collaboration; Community ecology; Conservation biology; Curriculum; Datasets; Deoxyribonucleic acid; DNA; DNA - analysis; DNA Barcoding, Taxonomic; Environment; Environmental DNA; Internet; Metadata; Microbiology - education; National parks; Principal Component Analysis; Researchers; Scientists; Software; Software Tool; Statistics as Topic; Studies; Taxonomy; Training; Visualization; Los Angeles California; California; United States > US; Channel Islands; metabarcoding; education; environmental DNA; community science; community ecology; citizen science; shiny; data visualization
• ISSN: 2046-1402; 2046-1402
• DOI: 10.12688/f1000research.16680.1

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.