Matlab Index

Matlab Directories

Matlab Files found in these Directories

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