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EditBoundaries.m functions findIdString and mapInRange Apr 30, 2018
FluxClustering.m
Genes_Sign.m test scripts and readme Jan 30, 2018
HGNC2symbol.mat
HMRcore.mat sbml of HRMcore Jan 28, 2018
HMRcore.xml
ReadME.asv test scripts and readme Jan 30, 2018
ReadME.md paper preprint link Feb 1, 2018
ReadME.txt test scripts and readme Jan 30, 2018
RepairNegFalse.m test scripts and readme Jan 30, 2018
ScFBAExpSetting.m charge field added in model structure Feb 1, 2018
convertTable_Cell.m test scripts and readme Jan 30, 2018
createPopModel.m test scripts and readme Jan 30, 2018
extractGeneRow.m functions findIdString and mapInRange Apr 30, 2018
findIdString.m functions findIdString and mapInRange Apr 30, 2018
getDataScored.m
getFluxes.m bug fixed Aug 23, 2018
getScore.m test scripts and readme Jan 30, 2018
integrateRAS.m
makeSCdataset.m test scripts and readme Jan 30, 2018
mapInRange.m functions findIdString and mapInRange Apr 30, 2018
replicateScFBAresults.m
scFBA.asv test scripts and readme Jan 30, 2018
scFBA_test.m
scoreSCdataset.m test scripts and readme Jan 30, 2018
setScFBABound.asv test scripts and readme Jan 30, 2018
single2IntPopModel.m
splitScFluxes.m test scripts and readme Jan 30, 2018

ReadME.md

scFBA (single-cell Flux Balance Analysis)

scFBA is a suite of MATLAB functions to perform a single-cell Flux Balance Analysis (scFBA).

scFBA includes all the functions that are necessary to predict single-cell fluxes from the following inputs:

  1. a Matlab matrix T including the scRNA-seq of Ncells single-cells, and (if available) of the bulk
  2. the SBML of a template metabolic network A

The final OUTPUT is a matrix including the flux of each reaction in each cell.

For information about the usage of each intermediate function, see the function Help.

An example of the pipeline usage is given in scFBA_test.m

The script replicateScFBAresults.m replicates all the results presented in Damiani et al, 2018.

REFERENCE:

  • Integration of single-cell RNA-seq data into metabolic models to characterize tumour cell populations - Authors: Chiara Damiani, Davide Maspero, Marzia Di Filippo, Riccardo Colombo, Dario Pescini, Alex Graudenzi, Hans Victor Westerhoff, Lilia Alberghina, Marco Vanoni and Giancarlo Mauri. 2018 (preprint: https://www.biorxiv.org/content/early/2018/01/30/256644)

SYSTEM REQUIREMENTS:

  • COBRA Toolbox 2017 is required
  • Gurobi solver is recommended, but scFBA works with any solver
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