proteomicsr: An analysis pipeline for label-based and label-free proteomics data

This package summarizes helpful functions to analyze global information on protein abundance (proteomics) and the abundance of post-translational modifications (PTMs), referred to as PTM-omics. Thereby, it supports data from label-free and label-based approaches. For this purpose, functions for initial data evaluation and clean-up, data transformation, determination of significantly affected candidates, and different typically presented proteomics plots are provided. Furthermore, it contains functions to perform enrichment analyses as well as to visualize significantly enriched terms as well as candidates assigned to such terms. Enrichment analyses are performed based on gene sets of the MSigDB, but also the visualization of results obtained using the Ingenuity Pathway Analysis (IPA, Qiagen) tool is possible. Last but not least, the steps necessary to perform a Weighted Gene Correlation Network Analysis (WGCNA) are included, starting with the network creation and finally exporting potential key drivers of the effects (so-called hub genes).

Although this package has been established for proteomics data, it works (in parts) for other omics layers as well. For instance, the determination of significantly altered candidates can be applied to metabolomics data, the enrichment using MSigDB gene sets can be applied to transcriptomics data, and the WGCNA is applicable to all omics layers, even for integrative data evaluation.