metagenomeSeq-deprecated-package	metagenomeSeq-deprecated
metagenomeSeq-package	metagenomeSeq-package
aggregateBySample	aggregateBySample
aggregateByTaxonomy	aggregateByTaxonomy
aggSamp	aggregateBySample
aggTax	aggregateByTaxonomy
biom2MRexperiment	biom2MRexperiment
calcNormFactors	calcNormFactors
calcPosComponent	calcPosComponent
calcShrinkParameters	calcShrinkParameters
calcStandardError	calcStandardError
calculateEffectiveSamples	calculateEffectiveSamples
calcZeroAdjustment	calcZeroAdjustment
calcZeroComponent	calcZeroComponent
colMeans,MRexperiment-method	MRexperiment-class
colSums,MRexperiment-method	MRexperiment-class
correctIndices	correctIndices
correlationTest	correlationTest
corTest	correlationTest
cumNorm	cumNorm
cumNormMat	cumNormMat
cumNormStat	cumNormStat
cumNormStatFast	cumNormStatFast
deprecated_metagenomeSeq_function	metagenomeSeq-deprecated
doCountMStep	doCountMStep
doEStep	doEStep
doZeroMStep	doZeroMStep
exportMat	exportMat
exportMatrix	exportMat
exportStats	exportStats
expSummary	expSummary
expSummary,MRexperiment-method	expSummary
extractMR	extractMR
filterData	filterData
fitDO	fitDO
fitFeatureModel	fitFeatureModel
fitLogNormal	fitLogNormal
fitMeta	metagenomeSeq-deprecated
fitMultipleTimeSeries	fitMultipleTimeSeries
fitPA	fitPA
fitSSTimeSeries	fitSSTimeSeries
fitTimeSeries	fitTimeSeries
fitZeroLogNormal	fitZeroLogNormal
fitZig	fitZig
genusPlot	plotGenus
getCountDensity	getCountDensity
getEpsilon	getEpsilon
getNegativeLogLikelihoods	getNegativeLogLikelihoods
getPi	getPi
getZ	getZ
isItStillActive	isItStillActive
libSize	libSize
libSize,MRexperiment-method	MRexperiment-class
libSize<-	libSize-set
libSize<-,MRexperiment,numeric-method	libSize-set
loadBiom	loadBiom
loadMeta	loadMeta
loadMetaQ	loadMetaQ
loadPhenoData	loadPhenoData
load_biom	metagenomeSeq-deprecated
load_meta	metagenomeSeq-deprecated
load_metaQ	metagenomeSeq-deprecated
load_phenoData	metagenomeSeq-deprecated
lungData	lungData
makeLabels	makeLabels
mergeMRexperiments	mergeMRexperiments
mergeTable	mergeTable
metagenomeSeq	metagenomeSeq-package
metagenomeSeq-deprecated	metagenomeSeq-deprecated
metagenomicLoader	loadMeta
mouseData	mouseData
MRcoefs	MRcoefs
MRcounts	MRcounts
MRcounts,MRexperiment-method	MRcounts
MRexperiment-class	MRexperiment-class
MRexperiment2biom	MRexperiment2biom
MRfulltable	MRfulltable
MRtable	MRtable
newMRexperiment	newMRexperiment
normFactors	normFactors
normFactors,MRexperiment-method	MRexperiment-class
normFactors<-	normFactors-set
normFactors<-,MRexperiment,numeric-method	normFactors-set
phenoData	loadPhenoData
plotBubble	plotBubble
plotClassTimeSeries	plotClassTimeSeries
plotCorr	plotCorr
plotFeature	plotFeature
plotGenus	plotGenus
plotMRheatmap	plotMRheatmap
plotOrd	plotOrd
plotOTU	plotOTU
plotRare	plotRare
plotTimeSeries	plotTimeSeries
posteriorProbs	posteriorProbs
posteriorProbs,MRexperiment-method	posteriorProbs
qiimeLoader	loadMetaQ
returnAppropriateObj	returnAppropriateObj
rowMeans,MRexperiment-method	MRexperiment-class
rowSums,MRexperiment-method	MRexperiment-class
settings2	zigControl
ssFit	ssFit
ssIntervalCandidate	ssIntervalCandidate
ssPerm	ssPerm
ssPermAnalysis	ssPermAnalysis
trapz	trapz
ts2MRexperiment	ts2MRexperiment
uniqueFeatures	uniqueFeatures
zigControl	zigControl
[,MRexperiment,ANY,ANY,ANY-method	MRexperiment-class
[,MRexperiment-method	MRexperiment-class
