Overview
imputomics wraps multiple missing-value imputation methods and provides simulations for comparing their behavior. It supports R and Shiny interfaces for omics matrices, including metabolomics, with missingness-mechanism scenarios and error summaries.
What can this tool do?
Common uses
- Compare and apply missing-value imputation methods to metabolomics tables.
Scientific fit
Primary function
Statistical analysis
Other functions
Visualization and reporting
Analysis types
Metabolite profiling, Multi-omics
Data compatibility
Inputs
Feature or peak table
Outputs
Feature or peak table, Statistical results
Input formats
R numeric matrices or tables containing missing values
Output formats
Imputed matrices, simulation/evaluation summaries and Shiny plots
Scope and considerations
Designed for
- An R package and Shiny application for simulating and imputing missing values across omics datasets, including metabolomics, with multiple imputation algorithms and evaluation utilities.
Not designed for
- Recovering the true unmeasured concentration with certainty or proving that simulated missingness matches the study mechanism.
Important requirements
- R and the selected method's dependencies; a numeric data matrix with correctly represented missing values and suitable evaluation data for simulation-based comparison.
Considerations
- Choose imputation assumptions using acquisition and preprocessing context. Prevent train/test leakage and evaluate how imputation changes downstream statistics rather than comparing reconstruction error alone.
Access and documentation
GPL-3.0 according to package DESCRIPTION. The hosted server and underlying imputation packages have separate operational and dependency requirements; local analysis avoids uploading study data.
License: GPL-3.0
Evidence and review
Enveda intake rechecked against official repository documentation, package/license metadata and primary publication identity on 2026-10-27. Editorial source review only; no software execution or independent benchmark. See docs/enveda-expansion-review-2026-10-27-batch2.md.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- imputomics: web server and R package for missing values imputation in metabolomics data. Bioinformatics (2024). doi:10.1093/bioinformatics/btae098
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-10-27 · First committed entry
Add 24 reviewed Enveda tools in a separate second batch
View change · Entry at this revision