Code and processed data for generating figures in the VIP2B paper

README for VIP2B Figure Folders================================ General Notes-------------Each figure folder contains the data, intermediate results, scripts, or notebooks used to generate the corresponding main or supplementary figure panels. In most cases, the final plotting step is performed using the figure-specific Jupyter notebook provided in that folder.Some analyses require large input files, long-running jobs, or external software. For convenience, several folders already include processed or summarized results that can be used directly for plotting. Use of This Repository----------------------------------1. Figure 1 folder contains nothing but serves as a folder placeholder since Figure 1 is the workflow.2. Use Figure 2 and Figure 3 folders to review benchmarking analyses for taxonomic and functional profiling, respectively.3. Use Figure 4 to examine paired bulk and VLP comparisons.4. Use Figure 5 and Figure 6 folders to explore disease-associated virome features and diversity relationships.5. Use Figure 7 to review disease classification analyses.6. Use Figure 8 to examine virome community type analyses. Important Notes---------------- Some upstream analyses are computationally intensive and may require high-performance computing resources.- Some folders include precomputed results so that figures can be generated without rerunning all upstream analyses.- File paths in the original code may need to be updated if the analyses are rerun on a different system.- This simplified README is intended as a navigation guide. For exact reproducibility, refer to the original figure-specific README files and scripts.See README.txt for more details.