RomicsProcessor use case 1 (Bacillus Cereus Proteomics)

This dataset and accompanying code correspond to Use Case 1 from the manuscript "Reproducible-by-design: RomicsProcessor, a FAIR ecosystem for multi-omics and spatial-omics analysis". The primary goal of this use case is to provide a definitive, computational demonstration of the "reproducibility-by-design" framework implemented in the RomicsProcessor R package. The analysis demonstrates how a complete data-processing workflow can be programmatically captured and re-executed to produce bit-for-bit identical results, directly addressing the reproducibility crisis stemming from the fragility of traditional script-and-data-sharing models. The Romics_object that serves as digital artifact of the analysis is the following /03_output_files/romics_proteins.rda Experimental Context:The dataset consists of the proteomic response of the bacterium Bacillus cereus (ATCC 14579) grown in four distinct media environments: a standard laboratory Luria-Bertani (LB) medium, a gut-mimicking AOAC medium, a zucchini puree, and a soil extract. Dataset Contents and Structure: The repository is organized into three main directories: 01_source_files/: Contains the primary input files required to initiate the analysis. This includes the protein abundance matrix and feature annotation files generated by FragPipe, as well as the manually created metadata file describing the experimental design. 02_code.Rmd: Contains the R script used to perform the entire data processing and statistical analysis workflow described in the manuscript. This script demonstrates how to create the romics_object and apply filtering, normalization, and statistical functions. It also demonstrates the reproducibility functions. 03_output_files/: Contains the final, processed data artifacts generated by the code. The key file is romics_proteins.rda, which is the final, fully processed Romics_object. This single file encapsulates the original data, all processing steps, parameters, software dependencies, and final statistical results, serving as a complete and verifiable digital record of the analysis. Other files in this directory include exported figures and tables from the analysis.