{"id":21583181,"url":"https://github.com/tnaake/msquality","last_synced_at":"2025-06-23T01:06:52.837Z","repository":{"id":45938489,"uuid":"369539464","full_name":"tnaake/MsQuality","owner":"tnaake","description":null,"archived":false,"fork":false,"pushed_at":"2025-01-27T09:30:22.000Z","size":20037,"stargazers_count":7,"open_issues_count":3,"forks_count":0,"subscribers_count":2,"default_branch":"devel","last_synced_at":"2025-06-23T01:06:40.004Z","etag":null,"topics":["mass-spectrometry","metabolomics","proteomics","qc","r"],"latest_commit_sha":null,"homepage":"","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/tnaake.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,"zenodo":null}},"created_at":"2021-05-21T13:10:53.000Z","updated_at":"2025-01-27T09:11:18.000Z","dependencies_parsed_at":"2023-12-19T10:44:08.210Z","dependency_job_id":"730fe0c3-983e-460f-816e-bffd79fd1e4c","html_url":"https://github.com/tnaake/MsQuality","commit_stats":{"total_commits":268,"total_committers":3,"mean_commits":89.33333333333333,"dds":0.04104477611940294,"last_synced_commit":"d5a8db9418c2b4bd33d072389942e7a7ea7cef5e"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/tnaake/MsQuality","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tnaake%2FMsQuality","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tnaake%2FMsQuality/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tnaake%2FMsQuality/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tnaake%2FMsQuality/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tnaake","download_url":"https://codeload.github.com/tnaake/MsQuality/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tnaake%2FMsQuality/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":261392178,"owners_count":23151718,"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":["mass-spectrometry","metabolomics","proteomics","qc","r"],"created_at":"2024-11-24T14:18:29.285Z","updated_at":"2025-06-23T01:06:47.820Z","avatar_url":"https://github.com/tnaake.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MsQuality\n\n[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)\n![R-CMD-check-bioc](https://github.com/tnaake/MsQuality/workflows/R-CMD-check-bioc/badge.svg)\n[![codecov.io](http://codecov.io/github/tnaake/MsQuality/coverage.svg?branch=master)](http://codecov.io/github/tnaake/MsQuality?branch=main)\n[![license](http://img.shields.io/badge/license-GPL%20%28%3E=%203%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-3.0.html)\n\nCalculation of QC metrics from mass spectrometry data\n\n## Description\nData quality assessment is an integral part of preparatory data analysis \nto ensure sound biological information retrieval. \n\nWe present here the `MsQuality` package, which provides functionality to calculate\nquality metrics for mass spectrometry-derived, spectral data at the per-sample\nlevel. `MsQuality` relies on the [`mzQC`](https://github.com/HUPO-PSI/mzQC) \nframework of quality metrics defined by the Human Proteome \nOrganization-Proteomics Standards Intitiative (HUPO-PSI). These metrics \nquantify the quality of spectral raw files using a controlled vocabulary. \n\nThe package is especially addressed towards users that acquire \nmass spectrometry data on a large scale (e.g. data sets from clinical settings \nconsisting of several thousands of samples): while it is easier to control \nfor high-quality data acquisition in small-scale experiments, typically run\nin one or few batches, clinical data sets are often acquired over longer \ntime frames and are prone to higher technical variation that is often\nunnoticed. `MsQuality` tries to address this problem by calculating metrics that\ncan be stored along the spectral data sets (raw files or feature-extracted \ndata sets). `MsQuality`, thus, facilitates the tracking of shifts in data quality\nand quantifies the quality using multiple metrics. It should be thus easier\nto identify samples that are of low quality (high-number of missing values,\ntermination of chromatographic runs, low instrument sensitivity, etc.).\n\nThe `MsQuality` package allows to calculate low-level quality metrics that require\nminimum information on mass spectrometry data: retention time, m/z values, \nand associated intensities.\nThe list included in the `mzQC` framework is excessive, also including \nmetrics that rely on more high-level information, that might not be readily\naccessible from .raw or .mzML files, e.g. pump pressure mean, or rely\non alignment results, e.g. retention time mean shift, signal-to-noise ratio,\nprecursor errors (ppm). \n\nThe `MsQuality` package is built upon the `Spectra` and the `MsExperiment` package.\nMetrics will be calculated based on the information stored in a \n`Spectra` object, thus, the spectral data of each sample should be stored\nin one `Spectra` object. The `MsExperiment` serves as a container to \nstore the mass spectral data of multiple samples. `MsQuality` enables the user\nto calculate quality metrics both on `Spectra` and `MsExperiment` objects. \n\n\n## Contact \n\nYou are welcome to \n\n * write a mail to \u003cthomasnaake (at) googlemail (dot) com\u003e \n * submit suggestions and issues: \u003chttps://github.com/tnaake/MsQuality/issues\u003e\n * send a pull request: \u003chttps://github.com/tnaake/MsQuality/issues\u003e \n\n## Install\n\n`MsQuality` is available via Bioconductor. To install the package, users can\neither install from the \n[devel branch](https://bioconductor.org/packages/devel/bioc/html/MsQuality.html) \nor from the current \n[RELEASE branch](https://bioconductor.org/packages/release/bioc/html/MsQuality.html).\n\nTo install `MsQuality`, you have first to install the \n[`BiocManager`](https://www.bioconductor.org/install/) and\n[remotes](http://cran.r-project.org/web/packages/cran/index.html) \npackage: \n\n```r\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nif (!requireNamespace(\"remotes\", quietly = TRUE))\n    install.packages(\"remotes\")\n```\n\nInstall the `MsQuality` package then via\n\n```r\n## to install from Bioconductor\nBiocManager::install(\"MsQuality\")\n\n## to install the development version from GitHub\nBiocManager::install(\"tnaake/MsQuality\")\n```\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftnaake%2Fmsquality","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftnaake%2Fmsquality","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftnaake%2Fmsquality/lists"}