CircumSpectrum Data Directory and Files

This Zenodo archive provides the data folder required to run the CircumSpectrum framework. After downloading, users should place this folder inside the main CircumSpectrum directory obtained from the GitHub repository, replacing the previous "data" directory template. Important: Do not modify any directory names or the internal folder structure. The CircumSpectrum source code (src/) is configured to access these specific directories as part of its workflow. Changing them may cause errors or failed data imports. CircumSpectrum is a flux-based analysis framework that converts bulk and single-cell RNA-seq data into metabolic fingerprints using genome-scale models (GEMs) and machine learning. It integrates three main modules: RADAR – Reaction-level activity decomposition and flux analysis SOURIS – Single fingerprint comparison between two reference assays CORALIE – Multi-tier correlation and analysis of several fingerprints across reference assays The provided data resources enable full reproduction of the CircumSpectrum examples and benchmark analyses. Contents of the data folder include: Raw RNA-seq count matrices Normalized RNA-seq data RNA-seq datasets prepared for iMAT calibration Human and mouse genome-scale metabolic models (GEMs) Starting metabolite concentrations for iMAT simulations RADA-xCheck datasets for observational study and experimental applications Metabolic fingerprint model files Fingerprint preparation objects from xCheck analyses Reference metabolic flux assay data Preprocessed single-cell RNA-seq Seurat objects These files support reproducible metabolic modeling, benchmarking, and downstream applications using the CircumSpectrum pipeline.