Datasets and analysis codes for "Global identification of independently modulated genes in Streptococcus pneumoniae reveals transcriptional rewiring in antibiotic-adapted and antibiotic-sensitive strains"

This repository contains the datasets and analysis scripts associated with the study: “Global identification of independently modulated genes in Streptococcus pneumoniae reveals transcriptional rewiring in antibiotic-adapted and antibiotic-sensitive strains”. The repository includes:- JSON-formatted iModulon datasets generated from multiple Streptococcus pneumoniae transcriptomic compendia- Jupyter notebooks for iModulon activity calculation and figure visualization- Raw experimental growth-curve data associated with Figure 8 The provided notebooks enable reproduction of the iModulon analyses and figures presented in the manuscript. JSON datasets contain reference-centered log2(TPM+1) expression matrices, iModulon gene weights, sample-specific activities, and sample metadata compatible with the PyModulon framework. These files are provided to support transparency, reproducibility, and reuse of the transcriptomic analyses presented in this study.