The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking
Open accessAbstract
Summary: We have created a Shiny-based Web application, called Shiny-phyloseq , for dynamic interaction with microbiome data that runs on any modern Web browser and requires no programming, increasing the accessibility and decreasing the entrance requirement to using phyloseq and related R tools. Along with a data- and context-aware dynamic interface for exploring the effects of parameter and method choices, Shiny-phyloseq also records the complete user input and subsequent graphical results of a user’s session, allowing the user to archive, share and reproduce the sequence of steps that created their result—without writing any new code themselves. Availability and implementation : Shiny-phyloseq is implemented entirely in the R language. It can be hosted/launched by any system with R installed, including Windows, Mac OS and most Linux distributions. Information technology administrators can also host Shiny-phyloseq from a remote server, in which case users need only have a Web browser installed. Shiny-phyloseq is provided free of charge under a GPL-3 open-source license through GitHub at http://joey711.github.io/shiny-phyloseq/ . Contact : mcmurdie@alumni.stanford.edu .
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Cites
ggplot2: Elegant Graphics for Data Analysis
Wickham, H. (2009) · doi:10.1007/978-0-387-98141-3 · Cited by 14,447
Reproducible research in computational science
Peng, R. D. (2011) · Science · doi:10.1126/science.1213847 · Cited by 1,449 · cited 1×
“Ideally, published scientific analyses are completely reproducible in as easy a fashion as possible; and anything less represents an impediment to both progress and peer review (Peng, 2011).”
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Cited by
Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons
Lagkouvardos, I., Fischer, S., Kumar, N., & Clavel, T. (2017) · PeerJ · doi:10.7717/peerj.2836 · Cited by 429
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics
Escobar-Zepeda, A., Vera-Ponce de León, A., & Sanchez-Flores, A. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00348 · Cited by 363
Recent Past, Present, and Future of the Food Microbiome
De Filippis, F., Parente, E., & Ercolini, D. (2018) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-030117-012312 · Cited by 163
REPRODUCIBLE RESEARCH WORKFLOW IN R FOR THE ANALYSIS OF PERSONALIZED HUMAN MICROBIOME DATA
CALLAHAN, B., PROCTOR, D., RELMAN, D., FUKUYAMA, J., & HOLMES, S. (2016) · Biocomputing 2016 · doi:10.1142/9789814749411_0018 · Cited by 35
Self-citationParente, E., Zotta, T., & Ricciardi, A. (2022) · doi:10.1101/2022.01.19.476946 · Cited by 15
Metadata
- Authors
- McMurdie, P. J., & Holmes, S.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-09-26
- Volume
- 31
- Issue
- 2
- Pages
- 282-283
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2112320611
- Cited by
- 164
- References
- 2
- FWCI
- 15.30
- Type
- journal article
- Language
- en
- Open access
- hybrid
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