{"id":19630315,"url":"https://github.com/sneumann/xcms","last_synced_at":"2025-05-14T19:09:23.842Z","repository":{"id":15470469,"uuid":"18203808","full_name":"sneumann/xcms","owner":"sneumann","description":"This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis","archived":false,"fork":false,"pushed_at":"2025-05-05T05:16:13.000Z","size":148250,"stargazers_count":199,"open_issues_count":203,"forks_count":81,"subscribers_count":21,"default_branch":"devel","last_synced_at":"2025-05-05T06:26:54.624Z","etag":null,"topics":["bioconductor","feature-detection","mass-spectrometry","metabolomics","peak-detection","r"],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sneumann.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","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":"2014-03-28T07:03:48.000Z","updated_at":"2025-04-25T07:16:38.000Z","dependencies_parsed_at":"2023-02-18T04:16:08.811Z","dependency_job_id":"773e8ff1-a629-420a-8391-ec9e9822ec9e","html_url":"https://github.com/sneumann/xcms","commit_stats":{"total_commits":3411,"total_committers":58,"mean_commits":"58.810344827586206","dds":0.7669305189094107,"last_synced_commit":"05d5bead7985f1d731dbd1eb76999e3dffc0fa07"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sneumann%2Fxcms","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sneumann%2Fxcms/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sneumann%2Fxcms/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sneumann%2Fxcms/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sneumann","download_url":"https://codeload.github.com/sneumann/xcms/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254209859,"owners_count":22032897,"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","feature-detection","mass-spectrometry","metabolomics","peak-detection","r"],"created_at":"2024-11-11T12:00:52.412Z","updated_at":"2025-05-14T19:09:23.239Z","avatar_url":"https://github.com/sneumann.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![R-CMD-check-bioc](https://github.com/sneumann/xcms/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/sneumann/xcms/actions?query=workflow%3AR-CMD-check-bioc)\n[![codecov.io](https://codecov.io/github/sneumann/xcms/coverage.svg?branch=master)](https://codecov.io/github/sneumann/xcms?branch=master)\n[![Years in Bioconductor](http://www.bioconductor.org/shields/years-in-bioc/xcms.svg)](http://www.bioconductor.org/packages/release/bioc/html/xcms.html)\n[![Ranking by downloads](http://bioconductor.org/shields/downloads/release/xcms.svg)](https://bioconductor.org/packages/stats/bioc/xcms/)\n[![Bioconductor release build status](http://www.bioconductor.org/shields/build/release/bioc/xcms.svg)](http://www.bioconductor.org/packages/release/bioc/html/xcms.html)\n[![Bioconductor devel build status](http://www.bioconductor.org/shields/build/devel/bioc/xcms.svg)](http://www.bioconductor.org/checkResults/devel/bioc-LATEST/xcms.html)\n\n\n# The `xcms` package: pre-processing GC/LC-MS/MS data\n\nPlease see the [package documentation](https://sneumann.github.io/xcms/) for\nmore information and examples and [news](inst/NEWS) for the latest changes.\n\n\n## Version 4\n\nVersion 4 adds native support for the\n[Spectra](https://github.com/RforMassSpectrometry/Spectra) package to `xcms` and\nallows to perform the pre-processing on `MsExperiment` objects (from the\n[MsExperiment](https://github.com/RforMassSpectrometry/MsExperiment). The new\nsupported data containers (`Spectra`, `MsExperiment` and `XcmsExperiment`) allow\nmore flexible analyses and seamless future extensions to additional types of\ndata (such as ion mobility data). Ultimately, these changes will also allow\neasier integration of `xcms` with other R packages such as\n[MsFeatures](https://github.com/RforMassSpectrometry/MsFeatures) or\n[MetaboAnnotation](https://github.com/RforMassSpectrometry/MetaboAnnotation).\n\nWhile it is suggested that users switch to the newer data and result objects,\nall functionality from version 3 and before remain fully supported.\n\n\n## Version 3\n\nVersion \u003e= 3 of the `xcms` package are updated and partially re-written versions\nof the original `xcms` package. The version number *3* was selected to avoid\nconfusions with the `xcms2` (http://pubs.acs.org/doi/abs/10.1021/ac800795f)\nsoftware. While providing all of the original software's functionality, `xcms`\nversion \u003e= 3 aims at:\n\n1) Better integration into the Bioconductor framework:\n  - Make use and extend classes defined in the `MSnbase` package.\n  - Implement class versioning (Biobase's `Versioned` class).\n  - Use `BiocParallel` for parallel processing.\n2) Implementation of validation methods for all classes to ensure data\n   integrity.\n3) Easier and faster access to raw spectra data.\n4) Cleanup of the source code:\n  - Remove obsolete and redundant functionality (`getEIC`, `rawEIC` etc).\n  - Unify interfaces, i.e. implement a layer of base functions accessing all\n    analysis methods (which are implemented in C, C++ or R).\n5) Using a more consistent naming scheme of methods that follows established\n   naming conventions (e.g. `correspondence` instead of `grouping`).\n6) Update, improve and extend the documentation.\n7) Establishing a layer of base R-functions that interface all analysis\n   methods. These should take M/Z, retention time (or scan index) and intensity\n   values as input along with optional arguments for the downstream functions\n   (implemented in C, C++ or R). The input arguments should be basic R objects\n   (numeric vectors) thus enabling easy integration of analysis methods in other\n   R packages.\n8) The user interface's analysis methods should take the (raw) data object and a\n   parameter class, that is used for dispatching to the corresponding analysis\n   algorithm.\n9) Add unit tests.\n\nDiscussions and suggestions are welcome:\nhttps://github.com/sneumann/xcms/issues\n\n\n## Contribution\n\nContributions to the *xcms* package are more than welcome, whether under the\nform of ideas, documentation, code, packages, ... For a contribution guideline\nplease see the [guideline for the RforMassSpectrometry\ninitiative](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#contributions). For\na seamless integration, contributors are expected to adhere to the\n[RforMassSpectrometry coding\nsyle](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#coding-style).\n\n\n## Code of Conduct\n\nAs contributors and maintainers of the package, we pledge to respect all people\nwho contribute through reporting issues, posting feature requests, updating\ndocumentation, submitting pull requests or patches, and other activities. See\nthe [RforMassSpectrometry Code of\nConduct](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#code-of-conduct)\nfor more information.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsneumann%2Fxcms","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsneumann%2Fxcms","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsneumann%2Fxcms/lists"}