ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; referees: 1 approved, 2 approved with reservations]
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. Resul...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
F1000 Research Ltd
2018-11-01
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| Series: | F1000Research |
| Online Access: | https://f1000research.com/articles/7-1734/v1 |
| _version_ | 1819051863125786624 |
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| author | Gaurav S. Kandlikar Zachary J. Gold Madeline C. Cowen Rachel S. Meyer Amanda C. Freise Nathan J.B. Kraft Jordan Moberg-Parker Joshua Sprague David J. Kushner Emily E. Curd |
| author_facet | Gaurav S. Kandlikar Zachary J. Gold Madeline C. Cowen Rachel S. Meyer Amanda C. Freise Nathan J.B. Kraft Jordan Moberg-Parker Joshua Sprague David J. Kushner Emily E. Curd |
| author_sort | Gaurav S. Kandlikar |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-21T12:10:42Z |
| format | Article |
| id | doaj.art-16c72b067e8543a192dc05adbf29b006 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-21T12:10:42Z |
| publishDate | 2018-11-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-16c72b067e8543a192dc05adbf29b0062022-12-21T19:04:35ZengF1000 Research LtdF1000Research2046-14022018-11-01710.12688/f1000research.16680.118233ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; referees: 1 approved, 2 approved with reservations]Gaurav S. Kandlikar0Zachary J. Gold1Madeline C. Cowen2Rachel S. Meyer3Amanda C. Freise4Nathan J.B. Kraft5Jordan Moberg-Parker6Joshua Sprague7David J. Kushner8Emily E. Curd9Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USADepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USADepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USADepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USADepartment of Microbiology and Microbial Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USADepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USADepartment of Microbiology and Microbial Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USAChannel Islands National Park, National Park Service, Ventura, CA, USAChannel Islands National Park, National Park Service, Ventura, CA, USADepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USAEnvironmental 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.https://f1000research.com/articles/7-1734/v1 |
| spellingShingle | Gaurav S. Kandlikar Zachary J. Gold Madeline C. Cowen Rachel S. Meyer Amanda C. Freise Nathan J.B. Kraft Jordan Moberg-Parker Joshua Sprague David J. Kushner Emily E. Curd ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; referees: 1 approved, 2 approved with reservations] F1000Research |
| title | ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; referees: 1 approved, 2 approved with reservations] |
| title_full | ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; referees: 1 approved, 2 approved with reservations] |
| title_fullStr | ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; referees: 1 approved, 2 approved with reservations] |
| title_full_unstemmed | ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; referees: 1 approved, 2 approved with reservations] |
| title_short | ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; referees: 1 approved, 2 approved with reservations] |
| title_sort | ranacapa an r package and shiny web app to explore environmental dna data with exploratory statistics and interactive visualizations version 1 referees 1 approved 2 approved with reservations |
| url | https://f1000research.com/articles/7-1734/v1 |
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