ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations

F1000Res. 2018 Nov 1:7:1734. doi: 10.12688/f1000research.16680.1. eCollection 2018.

Abstract

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.

Keywords: citizen science; community ecology; community science; data visualization; education; environmental DNA; metabarcoding; shiny.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Biodiversity
  • Curriculum
  • DNA / analysis*
  • DNA Barcoding, Taxonomic
  • Environment*
  • Internet*
  • Microbiology / education
  • Principal Component Analysis
  • Software*
  • Statistics as Topic*

Substances

  • DNA

Associated data

  • figshare/10.6084/m9.figshare.7199477.v1
  • figshare/10.6084/m9.figshare.7199510.v1

Grants and funding

GSK and ZJG were supported by the US-NSF Graduate Research Fellowship [DEG No. 1650604]. NJBK was supported the National Science Foundation [DEB-1644641]. EEC, RSM, and the CALeDNA program are supported by the University of California President’s Research Catalyst Award [CA-16-376437].