{"id":17899312,"url":"https://github.com/matthewcarlucci/discorhythm","last_synced_at":"2025-06-23T11:35:59.712Z","repository":{"id":83455577,"uuid":"179596217","full_name":"matthewcarlucci/DiscoRhythm","owner":"matthewcarlucci","description":"An R Package for Discovering Rhythmicity in Biological Data with an Interactive Web Interface","archived":false,"fork":false,"pushed_at":"2022-03-07T22:28:44.000Z","size":2397,"stargazers_count":13,"open_issues_count":5,"forks_count":2,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-05-24T19:03:50.991Z","etag":null,"topics":["bioconductor","data-visualization","oscillations","package","r","rhythm-detection","webapp"],"latest_commit_sha":null,"homepage":"https://bioconductor.org/packages/DiscoRhythm","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/matthewcarlucci.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-04-05T00:21:05.000Z","updated_at":"2024-12-09T15:29:41.000Z","dependencies_parsed_at":null,"dependency_job_id":"df096774-4114-444a-9758-7d2569863192","html_url":"https://github.com/matthewcarlucci/DiscoRhythm","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/matthewcarlucci/DiscoRhythm","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthewcarlucci%2FDiscoRhythm","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthewcarlucci%2FDiscoRhythm/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthewcarlucci%2FDiscoRhythm/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthewcarlucci%2FDiscoRhythm/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/matthewcarlucci","download_url":"https://codeload.github.com/matthewcarlucci/DiscoRhythm/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthewcarlucci%2FDiscoRhythm/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":261469568,"owners_count":23163125,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioconductor","data-visualization","oscillations","package","r","rhythm-detection","webapp"],"created_at":"2024-10-28T15:57:55.815Z","updated_at":"2025-06-23T11:35:54.698Z","avatar_url":"https://github.com/matthewcarlucci.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# DiscoRhythm - Discovering Rhythmicity \u003cimg src=\"inst/app/www/disco_128.png\" align=\"right\" width=\"120\" /\u003e\n\n![build](https://bioconductor.org/shields/build/release/bioc/DiscoRhythm.svg)\n![in Bioc](https://bioconductor.org/shields/years-in-bioc/DiscoRhythm.svg)\n[![](https://img.shields.io/badge/doi-10.1093/bioinformatics/btz834-green.svg)](https://doi.org/10.1093/bioinformatics/btz834)\n\n## Overview\n\nA summary of DiscoRhythm from *[Carlucci M. et al, 2020](https://doi.org/10.1093/bioinformatics/btz834)* is presented below.\n\n![](inst/DiscoRhythm_Figure1.png)\n\n\u003e 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.\n\n-----------------------------------------------------\n\n## Getting Started\n\nThe web application can be accessed on the [DiscoRhythm public server](https://mcarlucci.shinyapps.io/discorhythm/).\n\nSee the [tutorial](https://bioconductor.org/packages/release/bioc/vignettes/DiscoRhythm/inst/doc/disco_workflow_vignette.html) for details on usage of the web application and R package.\n\nSee [DiscoRhythm on Bioconductor](https://bioconductor.org/packages/release/bioc/html/DiscoRhythm.html) for more details.\n\nUse the [issue board](https://github.com/matthewcarlucci/DiscoRhythm/issues) to provide feedback on DiscoRhythm (feature requests, bugs, and further questions).\n\n### R Package Installation\n\nFor local usage of DiscoRhythm, install the R package from Bioconductor:\n\n```\nif (!requireNamespace(\"BiocManager\", quietly=TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"DiscoRhythm\")\n```\n\nOr install the latest version from GitHub:\n\n```\nlibrary(devtools)\ninstall_github(\"matthewcarlucci/DiscoRhythm\", build_vignettes=TRUE)\n```\n\n### Usage with Docker\n\nIf [docker](https://docs.docker.com/install/) is installed, the \n[DiscoRhythm container on Docker Hub](https://hub.docker.com/r/mcarlucci/discorhythm) \ncan be used to run the DiscoRhythm web application. \n\n### Citation\n\n\u003eMatthew 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](https://doi.org/10.1093/bioinformatics/btz834)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmatthewcarlucci%2Fdiscorhythm","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmatthewcarlucci%2Fdiscorhythm","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmatthewcarlucci%2Fdiscorhythm/lists"}