Matlab Index

Matlab Directories

Matlab Files found in these Directories

FSEOF	expandModel	getObjectiveString	ravenCobraWrapper
INITStepDesc	exportForGit	getPathwayDimensions	readYAMLmodel
ManualINITTests	exportModel	getPhylDist	removeBadRxns
SBMLFromExcel	exportModelToSIF	getRxnsFromKEGG	removeGenes
addExchangeRxns	exportToExcelFormat	getRxnsFromMetaCyc	removeLowScoreGenes
addGenesRaven	exportToTabDelimited	getRxnsInComp	removeMets
addJavaPaths	extractMiriam	getToolboxVersion	removeRavenFromPath
addMets	fillGaps	getTransportRxns	removeReactions
addRavenToUserPath	fillGapsLargeTests	getWSLpath	replaceMets
addRxns	fillGapsSmallTests	getWoLFScores	reporterMetabolites
addRxnsGenesMets	findGeneDeletions	groupRxnScores	rescaleModelForINIT
addSpontaneousRxns	findRAVENroot	guessComposition	reverseRxns
addTransport	fitParameters	haveFlux	runDynamicFBA
analyzeSampling	fitTasks	hmmerTests	runINIT
blastPlusTests	followChanged	importExcelModel	runPhenotypePhasePlane
buildEquation	followFluxes	importExportTests	runProductionEnvelope
canConsume	ftINIT	importModel	runRobustnessAnalysis
canProduce	ftINITFillGaps	linkMetaCycKEGGRxns	runSimpleOptKnock
cdhitTests	ftINITFillGapsForAllTasks	loadSheet	scoreComplexModel
changeGeneAssoc	ftINITFillGapsMILP	loadWorkbook	scoreModel
changeGrRules	ftINITInternalAlg	mafftTests	setColorToMapRxns
changeRxns	gapReport	makeFakeBlastStructure	setExchangeBounds
checkFileExistence	generateNewIds	makeSomething	setOmicDataToRxns
checkFunctionUniqueness	getAllRxnsFromGenes	mapCompartments	setParam
checkInstallation	getAllSubGraphs	mapPathwayRxnNames	setRavenSolver
checkModelStruct	getAllowedBounds	markPathwayWithExpression	setTitle
checkProduction	getBlast	markPathwayWithFluxes	simplifyModel
checkRxn	getBlastFromExcel	mergeCompartments	solveLP
checkSolution	getColorCodes	mergeLinear	solveQP
checkTasks	getDiamond	mergeModels	solverTests
checkTasksTests	getElementalBalance	miriamTests	sortIdentifiers
cleanSheet	getEnzymesFromMetaCyc	modelAbilitiesTests	sortModel
closeModel	getEssentialRxns	modelConversionTests	standardizeGrRules
colorPathway	getExchangeRxns	modelCurationTests	standardizeModelFieldOrder
colorSubsystem	getExprForRxnScore	modelSortingTests	startup
combineMetaCycKEGGModels	getExpressionStructure	optimizeProb	tinitTests
compareMultipleModels	getFluxZ	parseFormulas	trimPathway
compareRxnsGenesMetsComps	getFullPath	parseHPA	tutorial1
constructEquations	getGenesFromGrRules	parseHPArna	tutorial2
constructMultiFasta	getGenesFromKEGG	parseRxnEqu	tutorial2_solutions
constructPathwayFromCelldesigner	getINITModel	parseScores	tutorial3
constructS	getINITSteps	parseTaskList	tutorial3_solutions
consumeSomething	getIndexes	permuteModel	tutorial4
contractModel	getKEGGModelForOrganism	plotAdditionalInfo	tutorial4_solutions
convertCharArray	getMD5Hash	plotLabels	tutorial5
convertToIrrev	getMetaCycModelForOrganism	predictLocalization	tutorial6
copyToComps	getMetsFromKEGG	prepINITModel	updateDocumentation
deleteUnusedGenes	getMetsFromMetaCyc	printFluxes	writeSheet
diamondTests	getMetsInComp	printModel	writeYAMLmodel
dispEM	getMinNrFluxes	printModelStats
drawMap	getModelFromHomology	printOrange
drawPathway	getModelFromKEGG	qMOMA
editMiriam	getModelFromMetaCyc	randomSampling