{"id":16698427,"url":"https://github.com/lgatto/rforproteomics","last_synced_at":"2025-03-17T00:33:49.944Z","repository":{"id":4606143,"uuid":"5749403","full_name":"lgatto/RforProteomics","owner":"lgatto","description":"Using R and Bioconductor packages for the analysis and comprehension of proteomics data.","archived":false,"fork":false,"pushed_at":"2023-05-12T06:00:44.000Z","size":277985,"stargazers_count":90,"open_issues_count":2,"forks_count":35,"subscribers_count":16,"default_branch":"main","last_synced_at":"2025-02-27T15:37:33.845Z","etag":null,"topics":["bioconductor","bioconductor-packages","mass-spectrometry","proteomics","proteomics-data","r","tutorial"],"latest_commit_sha":null,"homepage":"http://lgatto.github.io/RforProteomics","language":"TeX","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/lgatto.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}},"created_at":"2012-09-10T12:50:35.000Z","updated_at":"2025-01-04T20:14:48.000Z","dependencies_parsed_at":"2023-07-05T17:00:26.150Z","dependency_job_id":null,"html_url":"https://github.com/lgatto/RforProteomics","commit_stats":null,"previous_names":[],"tags_count":12,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lgatto%2FRforProteomics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lgatto%2FRforProteomics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lgatto%2FRforProteomics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lgatto%2FRforProteomics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lgatto","download_url":"https://codeload.github.com/lgatto/RforProteomics/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243835942,"owners_count":20355611,"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","bioconductor-packages","mass-spectrometry","proteomics","proteomics-data","r","tutorial"],"created_at":"2024-10-12T17:52:04.892Z","updated_at":"2025-03-17T00:33:49.191Z","avatar_url":"https://github.com/lgatto.png","language":"TeX","readme":"## Introduction\n\nThe\n[`RforProteomics` package](http://www.bioconductor.org/packages/release/data/experiment/html/RforProteomics.html)\ndistributes and extends the use-cases described in the _Using `R` and\nBioconductor for proteomics data analysis_ manuscript\n([pubmed](http://www.ncbi.nlm.nih.gov/pubmed/23692960) and\n[pre-print](http://arxiv.org/abs/1305.6559)).  The package illustrates\nhow `R` and a selection of dedicated packages that can be used to\naccess mass-spectrometry proteomics data, manipulate and visualise it,\nhow to process label-free and labelled quantitative data and how to\nanalyse the quantitation data.\n\nThe package will be updated beyond the content of the manuscript to\nkeep up-to-date with progress in the area.  The\n[github page](https://github.com/lgatto/RforProteomics) can be used to\nedit the wiki and file new issues related to the package itself of\ngeneral needed for proteomics that should be addressed in `R`.\n\n\u003e **NB**: I you are interested in R packages for mass\n\u003e spectrometry-based proteomics and metabolomics, see also the [R for\n\u003e Mass Spectrometry initiative](https://www.rformassspectrometry.org/)\n\u003e packages and the [tutorial\n\u003e book](https://rformassspectrometry.github.io/docs/)\n\n\nIt would be great if this work could stimulate a wider participation\nto use `R` and develop `R` packages for proteomics and promote\ninteraction between computational biologists working in the field of\nproteomics, in particular by facilitating interoperability between\ntheir software.  The official [Bioconductor support\nsite](https://support.bioconductor.org/) is the channel of choice to\nask questions about specific Bioconductor packages.\n\n## Data and vignette\n\nThe package uses the\ndataset\n[`PXD000001`](http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000001) from\nthe [ProteomeXchange](http://www.proteomexchange.org/) repository in\nseveral examples. The data can be queried and downloaded from `R` with\nthe\n[`rpx`](http://bioconductor.org/packages/release/bioc/html/rpx.html)\npackage. The `RforProteomics` vignette is a detailed document\ncontaining the exact code to reproduce all the analyses presented in\nthe manuscript as well as other application examples. It can be\naccessed once the package is installed (see below) with the\n`RforProteomics()` function. Alternatively, the vignettes can be read\nonline\n[here](https://lgatto.github.io/RforProteomics/articles/RforProteomics.html) and\n[here](https://lgatto.github.io/RforProteomics/articles/RProtVis.html).\n\nA second vignette, `RProtVis` focuses on the visualisation of mass\nspectrometry and proteomics data with `R` and Bioconductor. From `R`,\nit is currently only available with Bioconductor `\u003e= 3.0` using the\n`RProtViz()` function. It can also be consulted\n[on-line](http://bioconductor.org/packages/release/data/experiment/vignettes/RforProteomics/inst/doc/RProtVis.html)\non the 'RforProteomics' development version page.\n\n## Installation\n\nThe package is available on\n[Bioconductor](http://bioconductor.org/packages/release/data/experiment/html/RforProteomics.html)\n(version \u003e= 2.13). To install the package and its documentation, start\n`R` (\u003e= `3.0.0` required) and type:\n\n```\nif (!requireNamespace(\"BiocManager\", quietly=TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"RforProteomics\")\n```\n\nTo install all dependencies (75+ packages, including `RforProteomics`)\nand fully reproduce the code in the vignettes, replace the last line\nin the code chunk above with:\n\n```\nBiocManager::install(\"RforProteomics\", dependencies = TRUE)\n```\n\n## Collaborative editing\n\nThe community and package authors are invited to contribute to the\npackage. If you have or know of a package of interest, please\n[fork](https://help.github.com/articles/fork-a-repo) the\n[repository](https://github.com/lgatto/RforProteomics), add a new\nsection to the vignette and send a\n[pull request](https://help.github.com/articles/creating-a-pull-request). If\nyou update the vignette, please also add yourself as a contributor to\nthe package.\n\n## Help\n\nTo obtain help or additional information about the `RforProteomics`\npackage and about the packages presented in the vignette or\nmanuscript, please use the [Bioconductor support\nsite](https://support.bioconductor.org/).\n\nFor general resources about `R`, see the corresponding section in the\nvignettes and the\n[TeachingMaterial](https://github.com/lgatto/TeachingMaterial)\nrepository.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flgatto%2Frforproteomics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flgatto%2Frforproteomics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flgatto%2Frforproteomics/lists"}