DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity Article Swipe
Matthew Carlucci
,
Algimantas Kriščiūnas
,
Haohan Li
,
Povilas Gibas
,
Karolis Koncevičius
,
Artūras Petronis
,
Gabriel Oh
·
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btz834
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btz834
Motivation Biological rhythmicity is fundamental to almost all organisms on Earth and plays a key role in health and disease. Identification of oscillating signals could lead to novel biological insights, yet its investigation is impeded by the extensive computational and statistical knowledge required to perform such analysis. Results To address this issue, we present DiscoRhythm (Discovering Rhythmicity), a user-friendly application for characterizing rhythmicity in temporal biological data. DiscoRhythm is available as a web application or an R/Bioconductor package for estimating phase, amplitude and statistical significance using four popular approaches to rhythm detection (Cosinor, JTK Cycle, ARSER and Lomb-Scargle). We optimized these algorithms for speed, improving their execution times up to 30-fold to enable rapid analysis of -omic-scale datasets in real-time. Informative visualizations, interactive modules for quality control, dimensionality reduction, periodicity profiling and incorporation of experimental replicates make DiscoRhythm a thorough toolkit for analyzing rhythmicity. Availability and implementation The DiscoRhythm R package is available on Bioconductor (https://bioconductor.org/packages/DiscoRhythm), with source code available on GitHub (https://github.com/matthewcarlucci/DiscoRhythm) under a GPL-3 license. The web application is securely deployed over HTTPS (https://disco.camh.ca) and is freely available for use worldwide. Local instances of the DiscoRhythm web application can be created using the R package or by deploying the publicly available Docker container (https://hub.docker.com/r/mcarlucci/discorhythm). Supplementary information Supplementary data are available at Bioinformatics online.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/bioinformatics/btz834
- OA Status
- hybrid
- Cited By
- 64
- References
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- Related Works
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- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2987116017Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/bioinformatics/btz834Digital Object Identifier
- Title
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DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicityWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2019Year of publication
- Publication date
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2019-11-06Full publication date if available
- Authors
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Matthew Carlucci, Algimantas Kriščiūnas, Haohan Li, Povilas Gibas, Karolis Koncevičius, Artūras Petronis, Gabriel OhList of authors in order
- Landing page
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https://doi.org/10.1093/bioinformatics/btz834Publisher landing page
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YesWhether a free full text is available
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hybridOpen access status per OpenAlex
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https://doi.org/10.1093/bioinformatics/btz834Direct OA link when available
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Computer science, R package, World Wide Web, Software package, Web application, Software, Data science, Programming languageTop concepts (fields/topics) attached by OpenAlex
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64Total citation count in OpenAlex
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2025: 14, 2024: 21, 2023: 13, 2022: 10, 2021: 3Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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