{"id":32110944,"url":"https://github.com/katjadanielzik/metabodynamics","last_synced_at":"2025-10-20T14:07:56.205Z","repository":{"id":257595618,"uuid":"838757066","full_name":"KatjaDanielzik/MetaboDynamics","owner":"KatjaDanielzik","description":"MetaboDynamics: a framework of probabilistic models to analyze longitudinal metabolomics data","archived":false,"fork":false,"pushed_at":"2025-10-01T08:55:27.000Z","size":139468,"stargazers_count":5,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-10-01T10:16:29.511Z","etag":null,"topics":["dynamics","functional-analysis","longitudinal-analysis","metabolomics-data","metabolomics-pipeline"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/KatjaDanielzik.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-08-06T09:28:10.000Z","updated_at":"2025-10-01T08:16:38.000Z","dependencies_parsed_at":"2024-09-17T16:49:18.008Z","dependency_job_id":"665bba08-a6b0-456f-b8d5-82775526f862","html_url":"https://github.com/KatjaDanielzik/MetaboDynamics","commit_stats":null,"previous_names":["katjadanielzik/metabodynamics"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/KatjaDanielzik/MetaboDynamics","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KatjaDanielzik%2FMetaboDynamics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KatjaDanielzik%2FMetaboDynamics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KatjaDanielzik%2FMetaboDynamics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KatjaDanielzik%2FMetaboDynamics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KatjaDanielzik","download_url":"https://codeload.github.com/KatjaDanielzik/MetaboDynamics/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KatjaDanielzik%2FMetaboDynamics/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280102837,"owners_count":26272420,"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","status":"online","status_checked_at":"2025-10-20T02:00:06.978Z","response_time":62,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["dynamics","functional-analysis","longitudinal-analysis","metabolomics-data","metabolomics-pipeline"],"created_at":"2025-10-20T14:07:51.805Z","updated_at":"2025-10-20T14:07:56.192Z","avatar_url":"https://github.com/KatjaDanielzik.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# MetaboDynamics:\n[![](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)\n[![](https://img.shields.io/badge/doi-10.18129/B9.bioc.MetaboDynamics%20-yellow.svg)](https://doi.org/10.18129/B9.bioc.MetaboDynamics )\n[![License: GPL](https://img.shields.io/badge/license-GPL-blue.svg)](https://cran.r-project.org/web/licenses/GPL)\n\n\nMetaboDynamics provides a framework of Bayesian models for robust and\neasy analysis of longitudinal metabolomics Data. It takes concentration\ntables with at least three replicates and KEGG IDs of metabolites as input\nand provides robust estimation of mean concentrations, functional enrichment\nanalysis employing the KEGG database and comparison of clusters of metabolite\ndynamics patterns (“dynamics clusters”) under different biological\nconditions.\n\n## Installation\n\nMetaboDynamics is an [R](https://cran.r-project.org/) package available\nfrom [Bioconductor](https://www.bioconductor.org).\n\nURL: https://www.bioconductor.org/packages/release/bioc/html/MetaboDynamics.html \n\nTo install MetaboDynamics, start R (4.5) and enter:\n\n``` r\nif (!require(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\"MetaboDynamics\")\n```\nYou can also install the development version (current bug fixes and added features\ncan be found in the [NEWS](https://github.com/KatjaDanielzik/MetaboDynamics/blob/main/inst/NEWS.md) \nfile) of MetaboDynamics:\n\n``` r\nif (!require(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(version=\"devel\")\nBiocManager::install(\"MetaboDynamics\")\n```\n\n## Overview\n\nMetaboDynamics facilitates the analysis of longitudinal metabolomics\ndata e.g. from untargeted LC-MS. Common tools mostly only allow the comparison\nbetween two time points instead of analyzing the full observed dynamics profile\nof metabolite concentrations over multiple time points. Furthermore common tools\nmostly only allow to compare two experimental conditions and are using \nfrequentist statistical methods. As metabolomics data is often noisy, robust \nmethods for the estimation of mean metabolite concentrations per time point\nare needed. \n\nMetaboDynamics allows longitudinal analysis over\nmultiple time points and experimental conditions employing three\nprobabilistic models:\n\n1)  A hierarchical Bayesian model for the robust estimation of means at\n    every time point despite varying spread between time points.Hierarchical\n    Bayesian models are known to balance between over- and underfitting, allowing\n    to gain as much information from the noisy data as possible while not being overly\n    confident about the estimates. Its outputs are A) differences between time \n    points for every metabolite (differential concentrations),\n    and B) metabolite specific dynamics profiles that can be used for\n    clustering.\n\n2)  Over-representation analysis of KEGG-functional modules such as Amino acid\n    metabolism or KEGG pathways in dynamics clusters with a quantitative model \n    that employs a hypergeometric distribution and reports probabilities of a \n    functional module or pathway being over-represented in a cluster. Can also \n    estimate under-representation of functional modules.\n\n3)  Estimation of the dynamics similarity between metabolite clusters of \n    different experimental conditions with a Bayesian model. This model infers \n    the mean pairwise Euclidean distance of composing metabolite dynamics between \n    two clusters (i.e. every metabolite dynamics from cluster A is compared with \n    every metabolite dynamics of cluster B). In combination with the comparison of \n    metabolites that compose two clusters this allows to spot differences and similarities between\n    experimental conditions. For examples clusters of metabolites with similar\n    metabolite composition but different dynamics between experimental conditions.\n\n## Workflow\n\nFor a worked example on simulated data see [Vignette](https://www.bioconductor.org/packages/devel/bioc/vignettes/MetaboDynamics/inst/doc/MetaboDynamics.html) or if package is installed:\n\n``` r\nbrowseVignettes(\"MetaboDynamics\")\n```\n\n![](man/figures/README-MetaboDynamics_pitch.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkatjadanielzik%2Fmetabodynamics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkatjadanielzik%2Fmetabodynamics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkatjadanielzik%2Fmetabodynamics/lists"}