Metabo Tools

Try the Demo

Load one of the example datasets below to explore the app before uploading your own data.

Upload Feature Data

Choose Feature Data File (.csv or .xlsx)

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Preview:

Upload Sample Metadata

Choose Sample Metadata File (.csv or .xlsx)

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Preview:

Configure FeatureData

Select Feature Name Column:

Select Columns to Drop:

Configure Sample Data

Select Batch Variable Column:

Select Sample Name Column:

My data has a biological variable of interest

Select Biological Variable Column:

Step 1: Preview Sample Matching

Step 2: Preprocessing

Filtering and imputation:

Filter features with >50% missing values

Impute remaining missing values (KNN)

Filter low-variance features (IQR)

Remove bottom X% lowest variance features:

Sample normalization:

Method:

Log2 transformation will always be applied after sample normalization.

Step 3: PCA Before Batch Correction

Batch Correction + Scaling

ComBat will be applied to your log2-normalized data. Select a scaling method to apply after batch correction. The same scaling will also be applied to the non-batch-corrected data so you have both versions available in your download.

Scaling method:

PCA after batch correction and scaling:

About Metabo Tools

Metabo Tools is a web application for metabolomics data preprocessing and batch correction.

This tool is currently under active development and testing. Please use results with appropriate caution and report any issues.

Source Code

The source code is available on GitHub:

https://github.com/UFHCC-BCBSR/app-metabo-tools

Contact

For questions, feedback, or to report issues, contact: hkates@ufl.edu

Developed in partnership with SECIM

This tool was developed in partnership with the University of Florida Southeast Center for Integrated Metabolomics (SECIM) .

University of Florida Health Cancer Center — Biostatistics, Computational Biology, and Bioinformatics Shared Resource (BCBSR)

Download Results

Download your complete results package. The Excel file contains all processed data versions and a README sheet. The HTML report contains a methods paragraph, processing log, file guide, and PCA plots for your records.

Download Excel Data Package

Download HTML Report

Complete batch correction to enable downloads.