{"id":13681043,"url":"https://github.com/lgatto/MSnbase","last_synced_at":"2025-04-30T03:30:30.340Z","repository":{"id":1097408,"uuid":"956680","full_name":"lgatto/MSnbase","owner":"lgatto","description":"Base Classes and Functions for Mass Spectrometry and Proteomics","archived":false,"fork":false,"pushed_at":"2025-04-11T05:28:53.000Z","size":113048,"stargazers_count":131,"open_issues_count":11,"forks_count":46,"subscribers_count":13,"default_branch":"master","last_synced_at":"2025-04-14T14:59:40.299Z","etag":null,"topics":["bioconductor","bioinformatics","mass-spectrometry","proteomics","proteomics-data","r","visualisation"],"latest_commit_sha":null,"homepage":"http://lgatto.github.io/MSnbase/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"shutterstock/rickshaw","license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lgatto.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","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":"2010-10-02T15:27:36.000Z","updated_at":"2025-04-11T05:28:58.000Z","dependencies_parsed_at":"2023-01-13T10:56:23.508Z","dependency_job_id":"f8a4e200-5367-445d-8467-b72caff04564","html_url":"https://github.com/lgatto/MSnbase","commit_stats":{"total_commits":3452,"total_committers":43,"mean_commits":80.27906976744185,"dds":0.6575898030127463,"last_synced_commit":"3fd84a57543c502631eaacd98dd8f79b2281fc62"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lgatto%2FMSnbase","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lgatto%2FMSnbase/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lgatto%2FMSnbase/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lgatto%2FMSnbase/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lgatto","download_url":"https://codeload.github.com/lgatto/MSnbase/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251634992,"owners_count":21619122,"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","bioinformatics","mass-spectrometry","proteomics","proteomics-data","r","visualisation"],"created_at":"2024-08-02T13:01:25.415Z","updated_at":"2025-04-30T03:30:29.641Z","avatar_url":"https://github.com/lgatto.png","language":"R","funding_links":[],"categories":["5. Raw Data Analysis"],"sub_categories":["Table of Contents"],"readme":"[![codecov.io](https://codecov.io/github/lgatto/MSnbase/coverage.svg?branch=master)](https://codecov.io/github/lgatto/MSnbase?branch=master)\n[![R-CMD-check-bioc](https://github.com/lgatto/MSnbase/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/lgatto/MSnbase/actions?query=workflow%3AR-CMD-check-bioc)\n\n\n# The `MSnbase` package\n\n\u003cimg align = \"right\" src=\"https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/MSnbase/MSnbase.png\" height=\"200\"\u003e\n\n[**MSnbase**](https://lgatto.github.io/MSnbase/) is an R/Bioconductor\npackage that provides infrastructure for plotting, manipulation and\nprocessing mass spectrometry and proteomics data. The project was\nstarted by [Laurent Gatto](https://lgatto.github.io/) in October 2010\n(Mon Oct 4 23:35:23 2010, according to the git log) and has, since\nthen, benefited from\n[various contributions](https://lgatto.github.io/msnbase-contribs/), in\nparticular [Sebastian Gibb](https://sebastiangibb.de/)\nand [Johannes Rainer](https://github.com/jorainer).\n\nThe official package page is the Bioconductor landing page\n([release](https://www.bioconductor.org/packages/release/bioc/html/MSnbase.html) or\n[devel](https://www.bioconductor.org/packages/devel/bioc/html/MSnbase.html) versions). The\n[github page](https://github.com/lgatto/MSnbase) page is for active\ndevelopment, issue tracking and forking/pulling purposes.\n\nTo get an overview of the package, see the\n[*MSnbase-demo*](https://lgatto.github.io/MSnbase/articles/v01-MSnbase-demo.html)\nvignette. More vignettes are available in the *Articles* tab.\n\n## The R for Mass Spectrometry initiative\n\nThe aim of the *R for Mass Spectrometry* initiative is to provide\nefficient, thoroughly documented, tested and flexible R software for\nthe analysis and interpretation of high throughput mass spectrometry\nassays, including proteomics and metabolomics experiments. The project\nformalises the longtime collaborative development efforts of its core\nmembers under the R for Mass Spectrometry organisation to facilitate\ndissemination and accessibility of their work.\n\nIf you are using MSnbase, consider switching to the **R for Mass\nSpectrometry** packages, in particular,\n[Spectra](https://rformassspectrometry.github.io/Spectra/) for raw\ndata, [PSMatch](https://rformassspectrometry.github.io/PSMatch/) for\nidentification data, and\n[QFeatures](https://rformassspectrometry.github.io/QFeatures/) for\nquantitative data. See https://RforMassSpectrometry.org for details.\n\n## Installation\n\nTo install the package:\n\n\n```r\ninstall.packages(\"BiocManager\")\nBiocManager::install(\"MSnbase\")\n```\n\nIf you need the github version (not recommended unless you know what\nyou are doing), use\n\n\n```r\nBiocManager::install(\"lgatto/MSnbase\")\n```\n\n## Questions\n\nGeneral questions should be asked on\nthe [Bioconductor support forum](https://support.bioconductor.org/),\nusing `MSnbase` to tag the question. Feel also free to open a\nGitHub [issue](https://github.com/lgatto/MSnbase/issues), in\nparticular for bug reports.\n\n## Citation\n\nTo cite the `MSnbase` package in publications, please use:\n\n\u003e Gatto L, Lilley KS. *`MSnbase` - an R/Bioconductor package for\n\u003e isobaric tagged mass spectrometry data visualization, processing and\n\u003e quantitation*. Bioinformatics. 2012 Jan\n\u003e 15;28(2):288-9. doi:10.1093/bioinformatics/btr645. PubMed\n\u003e [PMID:22113085](https://www.ncbi.nlm.nih.gov/pubmed/22113085).\n\n\n\u003e *`MSnbase`, efficient and elegant R-based processing and\n\u003e visualisation of raw mass spectrometry data*. Laurent Gatto,\n\u003e Sebastian Gibb, Johannes Rainer. bioRxiv 2020.04.29.067868; doi:\n\u003e https://doi.org/10.1101/2020.04.29.067868\n\n\n## Contributing\n\nContributions to the package are more than welcome. If you want to\ncontribute to this package, you should follow the same conventions as\nthe rest of the functions. Please do get in touch (preferable opening\na [github issue](https://github.com/lgatto/MSnbase/issues/)) to\ndiscuss any suggestions. The\n[`MSnbase` development vignette](https://lgatto.github.io/MSnbase/articles/v05-MSnbase-development.html) gives\nsome background on the class infrastructure.\n\nPlease note that this project is released with a\n[Contributor Code of Conduct](https://github.com/lgatto/MSnbase/blob/master/CONDUCT.md). By\nparticipating in this project you agree to abide by its terms.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flgatto%2FMSnbase","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flgatto%2FMSnbase","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flgatto%2FMSnbase/lists"}