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However, extracting biological understanding from these data is an arduous task requiring multiple analysis platforms that are not adapted for automated high-dimensional data analysis. Here, we introduce an integrated pipeline that combines several R packages to extract high-level biological understanding from large-scale phosphoproteomic data by seamless integration with existing databases and knowledge resources. In a single run, PhosPiR provides data clean-up, fast data overview, multiple statistical testing, differential expression analysis, phosphosite annotation and translation across species, multilevel enrichment analyses, proteome-wide kinase activity and substrate mapping and network hub analysis. Data output includes graphical formats such as heatmap, box-, volcano- and circos-plots. This resource is designed to assist proteome-wide data mining of pathophysiological mechanism without a need for programming knowledge.<\/jats:p>","DOI":"10.1093\/bib\/bbab510","type":"journal-article","created":{"date-parts":[[2021,11,25]],"date-time":"2021-11-25T15:14:40Z","timestamp":1637853280000},"source":"Crossref","is-referenced-by-count":7,"title":["PhosPiR: an automated phosphoproteomic pipeline in R"],"prefix":"10.1093","volume":"23","author":[{"given":"Ye","family":"Hong","sequence":"first","affiliation":[{"name":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3908-2467","authenticated-orcid":false,"given":"Dani","family":"Flinkman","sequence":"additional","affiliation":[{"name":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"},{"name":"Lund University, Lund, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3639-979X","authenticated-orcid":false,"given":"Tomi","family":"Suomi","sequence":"additional","affiliation":[{"name":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3825-0967","authenticated-orcid":false,"given":"Sami","family":"Pietil\u00e4","sequence":"additional","affiliation":[{"name":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"}]},{"given":"Peter","family":"James","sequence":"additional","affiliation":[{"name":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"},{"name":"Lund University, Lund, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9717-5610","authenticated-orcid":false,"given":"Eleanor","family":"Coffey","sequence":"additional","affiliation":[{"name":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, 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