Frequently Asked Questions
Have questions? We've got answers. If you don't see your question here, feel free to reach out.
What data formats does MetaboNexus accept?
MetaboNexus is designed for flexibility. The Preprocessing Tool primarily targets the `.h5ad` format for cleaning raw data. The main analysis workflow accepts `.h5ad`, `.h5`, `.csv`, and `.xlsx` files. For tabular formats like CSV or XLSX, the data must be structured with spatial coordinates in the first two columns (named `x`/`X` and `y`/`Y`) and metabolite intensities in the subsequent columns.
Why are some options in the app disabled or grayed out?
The user interface follows a strict, logical progression to guide you through the analysis pipeline. You must complete and confirm the actions in one step to unlock the next. For example, you must define your file groups in Step 1 before you can select analyses in Step 2. This ensures the workflow is followed correctly.
The analysis seems slow. Can I speed it up?
Yes. Some analyses are computationally intensive, but MetaboNexus is built to use the full power of your machine. In the final configuration panel, you can find a parameter to adjust the number of CPU cores used for the analysis. Increasing this number can significantly speed up analysis time, especially for large datasets.
Why are there no results for a specific group or analysis?
This can happen for a few reasons. A common issue is incorrectly formatted input files that are missing the required `x` and `y` coordinate columns. Another possibility is that the statistical pre-filtering (e.g., T-test or ANOVA) was too stringent and resulted in zero significant metabolites passing the filter for that group or comparison. The `analysis_log.txt` file generated with your results will contain detailed information to help diagnose the issue.
Do I need to install Python or any other libraries to run MetaboNexus?
No. MetaboNexus is provided as a complete, standalone desktop application. You do not need to install Python or manage any external libraries, making it accessible even for users with no coding experience.
Does the application require an internet connection?
An internet connection is required on the first run only. The application needs to download necessary large assets, which include the deep-learning model for tissue prediction and the databases for pathway enrichment analysis. After this initial setup, the application can be run completely offline.
How do I cite MetaboNexus in my publication?
A manuscript describing MetaboNexus is currently in the process of being published. Until the paper is available, please cite the official website: https://metabonexus.tech.