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We developed<jats:italic>tidyproteomics<\/jats:italic>to facilitate basic analysis, improve data interoperability and potentially ease the integration of new processing algorithms, mainly through the use of a simplified data-object.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The R package<jats:italic>tidyproteomics<\/jats:italic>was developed as both a framework for standardizing quantitative proteomics data and a platform for analysis workflows, containing discrete functions that can be connected end-to-end, thus making it easier to define complex analyses by breaking them into small stepwise units. Additionally, as with any analysis workflow, choices made during analysis can have large impacts on the results and as such,<jats:italic>tidyproteomics<\/jats:italic>allows researchers to string each function together in any order, select from a variety of options and in some cases develop and incorporate custom algorithms.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p><jats:italic>Tidyproteomics<\/jats:italic>aims to simplify data exploration from multiple platforms, provide control over individual functions and analysis order, and serve as a tool to assemble complex repeatable processing workflows in a logical flow. Datasets in<jats:italic>tidyproteomics<\/jats:italic>are easy to work with, have a structure that allows for biological annotations to be added, and come with a framework for developing additional analysis tools. The consistent data structure and accessible analysis and plotting tools also offers a way for researchers to save time on mundane data manipulation tasks.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12859-023-05360-7","type":"journal-article","created":{"date-parts":[[2023,6,6]],"date-time":"2023-06-06T19:15:24Z","timestamp":1686078924000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization"],"prefix":"10.1186","volume":"24","author":[{"given":"Jeff","family":"Jones","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elliot J.","family":"MacKrell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting-Yu","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brett","family":"Lomenick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael L.","family":"Roukes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tsui-Fen","family":"Chou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,6,6]]},"reference":[{"key":"5360_CR1","doi-asserted-by":"publisher","first-page":"14","DOI":"10.3390\/proteomes8030014","volume":"8","author":"EJ Dupree","year":"2020","unstructured":"Dupree EJ, Jayathirtha M, Yorkey H, Mihasan M, Petre BA, Darie CC. 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