{"id":21044956,"url":"https://github.com/gauravpandeylab/metaclean","last_synced_at":"2025-03-13T22:11:46.682Z","repository":{"id":73090286,"uuid":"254204021","full_name":"GauravPandeyLab/MetaClean","owner":"GauravPandeyLab","description":null,"archived":false,"fork":false,"pushed_at":"2020-12-08T02:21:23.000Z","size":130,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-20T17:35:14.309Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/GauravPandeyLab.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-04-08T21:24:43.000Z","updated_at":"2023-08-24T17:51:24.000Z","dependencies_parsed_at":"2023-03-01T04:30:40.147Z","dependency_job_id":null,"html_url":"https://github.com/GauravPandeyLab/MetaClean","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/GauravPandeyLab%2FMetaClean","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/GauravPandeyLab%2FMetaClean/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/GauravPandeyLab%2FMetaClean/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/GauravPandeyLab%2FMetaClean/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/GauravPandeyLab","download_url":"https://codeload.github.com/GauravPandeyLab/MetaClean/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243489835,"owners_count":20299001,"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":[],"created_at":"2024-11-19T14:19:16.887Z","updated_at":"2025-03-13T22:11:46.676Z","avatar_url":"https://github.com/GauravPandeyLab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# **MetaClean**: Detection of Low-Quality Peaks in Untargeted LC-MS Metabolomics Data\nMetaClean utilizes 11 peak-quality metrics and 8 diverse machine learning algorithms to build a classifier to detect and flag low-quality peaks in untargeted metabolomics data. It is an R package and can be easily incorporated into existing untargeted LC-MS metabolomics pipelines that utilize the pre-processing software XCMS.\n\nThe 11 peak-quality metrics used by MetaClean are adapted from the following publications: \u003cbr /\u003e\nZhang, W., \u0026 Zhao, P. X. (2014). Quality evaluation of extracted ion chromatograms and chromatographic peaks in liquid chromatography/mass spectrometry-based metabolomics data. BMC Bioinformatics, 15(Suppl 11), S5. https://doi.org/10.1186/1471-2105-15-S11-S5 \u003cbr /\u003e\nEshghi, S. T., Auger, P., \u0026 Mathews, W. R. (2018). Quality assessment and interference detection in targeted mass spectrometry data using machine learning. Clinical Proteomics, 15. https://doi.org/10.1186/s12014-018-9209-x\n\n\n## Installation\nTo install MetaClean from this GitHub page, run the following command:\n```\nremotes::install_github(\"KelseyChetnik/MetaClean\")\n```\n\nOr install the latest stable CRAN version: \u003cbr /\u003e\nhttps://cran.r-project.org/package=MetaClean\n\n\n## Usage\nCheck out this [vignette](https://github.com/KelseyChetnik/MetaClean/blob/master/vignettes/MetaClean_WalkThrough.Rmd) for step-by-step instructions on how to use the MetaClean package.\n\n\n## Citation\nChetnik, K., Petrick, L. \u0026 Pandey, G. MetaClean: a machine learning-based classifier for reduced false positive peak detection in untargeted LC–MS metabolomics data. Metabolomics 16, 117 (2020). https://doi.org/10.1007/s11306-020-01738-3\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgauravpandeylab%2Fmetaclean","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgauravpandeylab%2Fmetaclean","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgauravpandeylab%2Fmetaclean/lists"}