README.md

METAFlux: Characterizing metabolism from bulk and single-cell RNA-seq data

Capabilities

• Use genome scale metabolic model and FBA (Flux balance analysis) to derive 13,082 metabolic fluxes for bulk and single cell RNA-seq datasets
• Discover different modes of metabolic cooperation and competition in single-cell RNA-seq data
• Enable massive public RNA-seq datasets mining in cancer metabolism

Check out the full paper for more detailed methods and applications: Characterizing metabolism from bulk and single-cell RNA-seq data using METAFlux

Installation

METAFlux R package can be easily installed from Github using devtools:

devtools::install_github('KChen-lab/METAFlux')

Installation of Other Dependencies

• Install the osqp package for optimization using install.packages('osqp'), If you encounter any issue during METAFlux installation.
• Install the dplyr package using install.packages('dplyr').
• For single cell data analysis, we provide pipeline to work with Seurat(Seurat V4). Please install Seurat package by install.packages('Seurat').

Tutorial

Please check out this link for a full tutorial on using METAFlux:

• Full tutorial using METFAFlux for bulk and single-cell RNA seq data analysis with detailed explanation