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.本Zenodo存档提供了运行CircumSpectrum框架所需的数据文件夹。下载完成后，用户需将该文件夹置于从GitHub仓库获取的CircumSpectrum主目录内，替换原有的"data"目录模板。 重要提示：请勿修改任何目录名称或内部文件夹结构。CircumSpectrum的源代码（src/）已配置为在其工作流程中访问这些特定目录，更改后可能导致错误或数据导入失败。 CircumSpectrum是一款基于通量的分析框架，可通过基因组规模模型（genome-scale models, GEMs）与机器学习，将批量及单细胞RNA测序（RNA-seq）数据转化为代谢指纹图谱。该框架集成了三大核心模块： - RADAR：反应水平活性分解与通量分析 - SOURIS：两份参考检测间的单指纹图谱比对 - CORALIE：多参考检测下多份指纹图谱的多层级关联与分析 本次提供的数据资源可完整复现CircumSpectrum的示例与基准分析流程。 数据文件夹包含以下内容： - 原始RNA-seq计数矩阵 - 标准化RNA-seq数据 - 用于iMAT校准的RNA-seq数据集 - 人类与小鼠基因组规模代谢模型（GEMs） - iMAT模拟所用的初始代谢物浓度 - 用于观测研究与实验应用的RADA-xCheck数据集 - 代谢指纹图谱模型文件 - 来自xCheck分析的指纹图谱制备对象 - 参考代谢通量检测数据 - 预处理后的单细胞RNA-seq Seurat对象 这些文件可支持基于CircumSpectrum流程的可复现代谢建模、基准测试及下游应用。