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Abstract

The Perseus software provides a comprehensive framework for the statistical analysis of large-scale quantitative proteomics data, also in combination with other omics dimensions. Rapid developments in proteomics technology and the ever-growing diversity of biological studies increasingly require the flexibility to incorporate computational methods designed by the user. Here, we present the new functionality of Perseus to integrate self-made plugins written in C#, R, or Python. The user-written codes will be fully integrated into the Perseus data analysis workflow as custom activities. This also makes language-specific R and Python libraries from CRAN (cran.r-project.org), Bioconductor (bioconductor.org), PyPI (pypi.org), and Anaconda (anaconda.org) accessible in Perseus. The different available approaches are explained in detail in this article. To facilitate the distribution of user-developed plugins among users, we have created a plugin repository for community sharing and filled it with the examples provided in this article and a collection of already existing and more extensive plugins. © 2020 The Authors. Basic Protocol 1: Basic steps for R plugins Support Protocol 1: R plugins with additional arguments Basic Protocol 2: Basic steps for python plugins Support Protocol 2: Python plugins with additional arguments Basic Protocol 3: Basic steps and construction of C# plugins Basic Protocol 4: Basic steps of construction and connection for R plugins with C# interface Support Protocol 4: Advanced example of R Plugin with C# interface: UMAP Basic Protocol 5: Basic steps of construction and connection for python plugins with C# interface Support Protocol 5: Advanced example of python plugin with C# interface: UMAP Support Protocol 6: A basic workflow for the analysis of label-free quantification proteomics data using perseus. © 2020 The Authors.