DiscoRhythm
An R Package for Discovering Rhythmicity in Biological Data with an Interactive Web Interface
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 9 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.2%) to scientific vocabulary
Keywords
Repository
An R Package for Discovering Rhythmicity in Biological Data with an Interactive Web Interface
Basic Info
- Host: GitHub
- Owner: matthewcarlucci
- Language: R
- Default Branch: master
- Homepage: https://bioconductor.org/packages/DiscoRhythm
- Size: 2.29 MB
Statistics
- Stars: 13
- Watchers: 4
- Forks: 2
- Open Issues: 5
- Releases: 0
Topics
Metadata Files
README.md
DiscoRhythm - Discovering Rhythmicity 
Overview
A summary of DiscoRhythm from Carlucci M. et al, 2020 is presented below.
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). [...] Informative visualizations, interactive modules for quality control, dimensionality reduction, periodicity profiling, and incorporation of experimental replicates make DiscoRhythm a thorough toolkit for analyzing rhythmicity.
Getting Started
The web application can be accessed on the DiscoRhythm public server.
See the tutorial for details on usage of the web application and R package.
See DiscoRhythm on Bioconductor for more details.
Use the issue board to provide feedback on DiscoRhythm (feature requests, bugs, and further questions).
R Package Installation
For local usage of DiscoRhythm, install the R package from Bioconductor:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("DiscoRhythm")
Or install the latest version from GitHub:
library(devtools)
install_github("matthewcarlucci/DiscoRhythm", build_vignettes=TRUE)
Usage with Docker
If docker is installed, the DiscoRhythm container on Docker Hub can be used to run the DiscoRhythm web application.
Citation
Matthew Carlucci, Algimantas Kriščiūnas, Haohan Li, Povilas Gibas, Karolis Koncevičius, Art Petronis, Gabriel Oh, DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity, Bioinformatics, Volume 36, Issue 6, 15 March 2020, Pages 1952–1954, https://doi.org/10.1093/bioinformatics/btz834
Owner
- Name: Matthew Carlucci
- Login: matthewcarlucci
- Kind: user
- Repositories: 7
- Profile: https://github.com/matthewcarlucci
GitHub Events
Total
- Watch event: 1
- Issue comment event: 1
Last Year
- Watch event: 1
- Issue comment event: 1
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Matthew Carlucci | m****6@g****m | 72 |
| PoGibas | p****s@g****m | 17 |
| Nitesh Turaga | n****a@g****m | 12 |
| Karolis Koncevičius | k****s@g****m | 1 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 7
- Total pull requests: 2
- Average time to close issues: 10 months
- Average time to close pull requests: about 23 hours
- Total issue authors: 7
- Total pull request authors: 2
- Average comments per issue: 1.86
- Average comments per pull request: 1.5
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- matthewcarlucci (1)
- albertdyu (1)
- JarrigeD (1)
- devang-mehta (1)
- Danvor (1)
- TeresaRubio (1)
- dzamila24 (1)
Pull Request Authors
- PoGibas (1)
- karoliskoncevicius (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 11,635 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: DiscoRhythm
Interactive Workflow for Discovering Rhythmicity in Biological Data
- Homepage: https://github.com/matthewcarlucci/DiscoRhythm
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/DiscoRhythm/inst/doc/DiscoRhythm.pdf
- License: GPL-3
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Latest release: 1.24.0
published 10 months ago