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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research » Research » Publications at this Location » Publication #360246

Research Project: Integrated Disease Management of Exotic and Emerging Plant Diseases of Horticultural Crops

Location: Horticultural Crops Research

Title: Referee report for: Ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations

Author
item Grunwald, Niklaus - Nik
item Foster, Zachary - Oregon State University

Submitted to: F1000Research
Publication Type: Other
Publication Acceptance Date: 12/18/2018
Publication Date: 12/19/2018
Citation: Grunwald, N.J., Foster, Z. 2018. Referee report for: Ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations. F1000Research. 7:1734. https://doi.org/10.5256/f1000research.18233.r40128.
DOI: https://doi.org/10.5256/f1000research.18233.r40128

Interpretive Summary:

Technical Abstract: We review the article describing the R package ranacapa that implements an interactive shiny web app available at https://gauravsk.shinyapps.io/ranacapa for exploration of environmental DNA characterized by amplicon sequencing. This app facilitates many of the standard tests and plots done for metabarcoding data. The app requires two dataset to run, namely a taxonomy-by-sample matrix file and a simple metadata file with descriptive information on the actual environmental samples. This package is particularly useful to anybody interested in exploring biome diversity but lacking extensive computational and bioinformatics skills. We appreciate the focus on open-source code and accessibility, in particular testing the app with Ubuntu and using the color-blind friendly viridis color palette. There are some minor changes in the style of plots and wording we would like to see, but these are a matter of opinion and do not affect the validity of the results. We feel this app is quite useful as is and it is described well in the associated article. We suggest many improvements that could be made, but most of these are intended as constructive suggestions.