Predicting interactions between phages and bacteria through proteome representation: inputs, outputs and parameters

Data and results for the LMU Munich bachelor's thesis "Predicting interactions between phages and bacteria through proteome representation" (Sinan Klein, 2026; supervised by Prof. Christian L. Müller). The study asks which of two kinds of phage–host links can be predicted from protein clusters shared between bacterial genera and viral OTUs (vOTUs):- Y: CRISPR-spacer links between a genus and a vOTU.- W: co-abundance edges from a SPIEC-EASI graphical-lasso network. The analysis covers three human gut cohorts: CRC, GvHD and IBD. The record contains the input tables the pipeline reads (inputs.zip), the complete outputs of run 20260916_152830 for each cohort (outputs_*.zip), the configuration (config.yaml) with an explanation of every parameter (PARAMETERS.md), and a README describing every file and how to reproduce the run. Code: https://github.com/SinanKlein/Bachelors_thesis (tag v1.0-thesis, commit 83a1bae)