Inferring a cell's capabilities from omics data with ImmCellFie
Helen O. MassoniD, David BorlandiD, Jason ReillyiD, Adrian Telleria, Shalki ShrivastavaiD, Matt Watson, Luthfi Bustillo, Zerong LiiD, Laura Capps, Benjamin P. KellmaniD, Zachary A. KingiD, Anne RichelleiD, Nathan E. LewisiD, Kimberly RobaskyiD
Abstract
ImmCellFie is a user-friendly, web-based platform for comprehensive analysis of metabolic functions inferred from transcriptomic or proteomic data. It enables researchers to leverage the powerful mechanistic insight provided by complex genome-scale metabolic models with little to no bioinformatics training required. The platform has been integrated with a series of useful tools and richly annotated scientific visualizations for interactive exploration by the user. ImmCellFie pushes beyond simple statistical enrichment and incorporates complex biological mechanisms to quantify cell activity. Graphical abstract
02 /Specification & Classification
Click any tag to browse matching papers- Citations
- 1
- Assay
- Research Focus
- Approach
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- What does your cell really do? Model-based assessment of mammalian cells metabolic functionalities using omics data
Anne Richelle, Benjamin P. Kellman, … Nathan E. Lewis·Cell Reports MethodsPeer-reviewed·Jun 30, 2021
- Inferring secretory and metabolic pathway activity from omic data with secCellFie
Helen O. Masson, Mojtaba Samoudi, … Nathan E. Lewis·Metabolic EngineeringPeer-reviewed·Jan 1, 2024
- Atlas-scale metabolic activities inferred from single-cell and spatial transcriptomics
Erick Armingol, James Ashcroft, … Roser Vento‐Tormo·bioRxiv·May 9, 2025
- Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions
Anne Richelle, Austin W.T. Chiang, … Nathan E. Lewis·PLoS Computational BiologyPeer-reviewed·Apr 15, 2019
- OmnibusX: A unified platform for accessible multi-omics analysis
Linh Truong, Thao Truong, Huy Nguyen·PLoS Computational BiologyPeer-reviewed·Sep 8, 2025
- Fast analyzing, exploring and sharing quantitative omics data using omicsViewer
Chen Meng·bioRxiv·Mar 10, 2022