Expanding the Perseus Software for Omics Data Analysis With Custom Plugins.

Expanding the Perseus Software for Omics Data Analysis With Custom Plugins. Curr Protoc Bioinformatics. 2020 Sep;71(1):e105 Authors: Yu SH, Ferretti D, Schessner JP, Rudolph JD, Borner GHH, Cox J 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...
Source: Current Protocols in Bioinformatics - Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research