Package: METAFLUX 2.2.0

METAFLUX: High-Performance Metabolic Flux Analysis from Bulk and Single-Cell RNA-seq Data

A performance-optimized implementation of METAFlux for characterizing cellular metabolism from bulk and single-cell RNA-sequencing data. Uses genome-scale metabolic modeling with Human-GEM to derive 13,082 metabolic fluxes through flux balance analysis (FBA). Features parallel computing, Rcpp acceleration, and optimized algorithms for 10-20x faster computation.

Authors:Zaoqu Liu [aut, cre], Yuefan Huang [aut], Kyle Tsai [aut]

METAFLUX_2.2.0.tar.gz
METAFLUX_2.2.0.zip(r-4.7)METAFLUX_2.2.0.zip(r-4.6)METAFLUX_2.2.0.zip(r-4.5)
METAFLUX_2.2.0.tgz(r-4.6-x86_64)METAFLUX_2.2.0.tgz(r-4.6-arm64)METAFLUX_2.2.0.tgz(r-4.5-x86_64)METAFLUX_2.2.0.tgz(r-4.5-arm64)
METAFLUX_2.2.0.tar.gz(r-4.7-arm64)METAFLUX_2.2.0.tar.gz(r-4.7-x86_64)METAFLUX_2.2.0.tar.gz(r-4.6-arm64)METAFLUX_2.2.0.tar.gz(r-4.6-x86_64)
METAFLUX_2.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
METAFLUX/json (API)

# Install 'METAFLUX' in R:
install.packages('METAFLUX', repos = c('https://zaoqu-liu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zaoqu-liu/metaflux/issues

Pkgdown/docs site:https://zaoqu-liu.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • bulk_test_example - Bulk test example
  • cell_medium - This file contains the hams medium nutrients information
  • human_blood - This file contains the hams medium nutrients information in human blood
  • human_gem - Human-GEM Metabolic Model Data
  • nutrient_lookup_files - 1648 exchange reactions:mathematical representation of uptake/secrete metabolites into the extracellular space
  • sc_test_example - Single cell test seurat object example

On CRAN:

Conda:

cpp

3.89 score 1 stars 31 scripts 5 exports 146 dependencies

Last updated from:00531df233 (on main). Checks:11 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR228
linux-devel-x86_64ERROR267
source / vignettesOK386
linux-release-arm64ERROR238
linux-release-x86_64ERROR266
macos-release-arm64ERROR202
macos-release-x86_64ERROR501
macos-oldrel-arm64ERROR250
macos-oldrel-x86_64ERROR413
windows-develERROR248
windows-releaseERROR216
windows-oldrelERROR210
wasm-releaseOK170

Exports:calculate_avg_expcalculate_reaction_scorecompute_fluxcompute_sc_fluxconstruct_flux_bounds

Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscommonmarkcowplotcpp11crosstalkcurldata.tabledeldirdigestdoParalleldotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomeforeachfsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemimeminiUInlmeopensslosqpotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS7sassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo

Bulk RNA-seq Metabolic Flux Analysis
Overview | Load Package and Data | Step 1: Calculate MRAS | MRAS Distribution | Step 2: Compute Metabolic Fluxes | Flux Interpretation | Step 3: Key Metabolic Indicators | Central Carbon Metabolism | Biomass Production | Step 4: Pathway Analysis | Step 5: Quality Control | Steady-State Verification | Gene Coverage | Summary | Author | Session Information
Rendered frombulk_analysis.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23

Visualization Guide for METAFLUX
Overview | Load Package and Data | Step 1: Calculate MRAS | Step 2: Compute Fluxes | Visualization 1: Flux Distribution | Visualization 2: Key Metabolite Exchange | Visualization 3: Top Variable Reactions | Visualization 4: Pathway Activity | Visualization 5: Sample Correlation | Visualization 6: Exchange Reaction Analysis | Summary Statistics | Session Information
Rendered fromvisualization.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23

Algorithm Theory and Mathematical Framework
Introduction | Theoretical Background | Genome-Scale Metabolic Models | Stoichiometric Matrix | Flux Balance Analysis (FBA) | Steady-State Assumption | Optimization Problem | Biomass Objective | Metabolic Reaction Activity Scores (MRAS) | Gene-Protein-Reaction (GPR) Rules | Scoring Algorithm | Isoenzyme Score (OR) | Complex Score (AND) | Mixed Relationships | Normalization | Flux Bounds Construction | Reversible Reactions | Irreversible Reactions | Exchange Reactions | Community Modeling (Single-Cell) | Community Stoichiometric Matrix | Weighted Objective | Solver: OSQP | Algorithm Settings | Convergence | Computational Complexity | References | Author
Rendered fromalgorithm.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23

Introduction to METAFLUX
Overview | Key Features | Author | Installation | From R-universe (Recommended) | From GitHub | Quick Start | Load Package | Bulk RNA-seq Analysis | Single-Cell Analysis | Workflow Overview | Data Requirements | Citation | Session Info
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23

Single-Cell RNA-seq Metabolic Flux Analysis
Overview | Biological Context | Tumor Microenvironment Metabolism | Community Modeling Concept | Data Preparation | Input Requirements | Load Example Data | Step 1: Bootstrap Aggregation | Bootstrap Algorithm | Step 2: Calculate MRAS | Step 3: Define Cell Type Fractions | Step 4: Community Flux Calculation | Output Structure | Step 5: Analyze Results | Extract Cell Type-Specific Fluxes | Compare Metabolic Phenotypes | External Medium Exchange | Advanced Analysis | Metabolic Competition | Metabolic Cooperation | Performance Tips | Parallel Computing | Memory Management | Biological Interpretation | Warburg Effect | Immunometabolism | Output Files | Next Steps | Author | Session Information
Rendered fromsinglecell_analysis.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23