Add2History	Add2History
addColors	QFeatures-excel
Add_Aggregated_rowData	DaparToolshed-aggregate-func
Add_Item_to_Dataset	Add_Item_to_Dataset
adjacency-matrix-filter	adjacency-matrix-filter
AdjMatFilters	adjacency-matrix-filter
aggQmetacell	DaparToolshed-aggregate-func
aggregateFeatures4Prostar	DaparToolshed-aggregate
aggregateFeatures4Prostar,QFeatures-method	DaparToolshed-aggregate
aggregateFeatures4Prostar,SummarizedExperiment-method	DaparToolshed-aggregate
aggregateMethods	DaparToolshed-aggregate-func
aggregateRedistribution	DaparToolshed-aggregateRedistribution
aggregateRedistribution,QFeatures-method	DaparToolshed-aggregateRedistribution
aggregateRedistribution,SummarizedExperiment-method	DaparToolshed-aggregateRedistribution
allPeptides	adjacency-matrix-filter
analysis	QFeatures-accessors
analysis,QFeatures-method	QFeatures-accessors
analysis,SummarizedExperiment-method	QFeatures-accessors
analysis<-	QFeatures-accessors
applyAnovasOnProteins	applyAnovasOnProteins
BuildAdjacencyMatrix	BuildAdjacencyMatrix
BuildColumnToProteinDataset	DaparToolshed-aggregate-func
buildGraph	buildGraph
BuildMetacell	BuildMetacell
checkConditions	checkConditions
checkDesign	checkDesign
Children	Children
classic1wayAnova	classic1wayAnova
CleanRowData	CleanRowData
compareNormalizationD_HC	compareNormalizationD_HC
compute_t_tests	compute_t_tests
ConnectedComp	QFeatures-accessors
ConnectedComp,QFeatures-method	QFeatures-accessors
ConnectedComp,SummarizedExperiment-method	QFeatures-accessors
ConnectedComp<-	QFeatures-accessors
ConvertListToHtml	ConvertListToHtml
CountPep	CountPep
createQFeatures	import-export-QFeatures
createSampleinfo	import-export-QFeatures
custom_metacell_colors	q_metacell
DaparToolsehd,	QFeatures-filtering-oneSE
DaparToolshed-aggregate	DaparToolshed-aggregate
DaparToolshed-aggregateRedistribution	DaparToolshed-aggregateRedistribution
design_qf	QFeatures-accessors
design_qf,QFeatures-method	QFeatures-accessors
design_qf<-	QFeatures-accessors
diffAnaComputeAdjustedPValues	diffAnaComputeAdjustedPValues
diffAnaComputeFDR	diffAnaComputeFDR
diffAnaVolcanoplot_rCharts	diffAnaVolcanoplot_rCharts
DifferentialAnalysis	QFeatures-accessors
DifferentialAnalysis,QFeatures-method	QFeatures-accessors
DifferentialAnalysis,SummarizedExperiment-method	QFeatures-accessors
DifferentialAnalysis<-	QFeatures-accessors
displayCCvisNet	displayCCvisNet
ExtendPalette	ExtendPalette
ExtractUniquePeptides	ExtractUniquePeptides
filename	QFeatures-accessors
filename,QFeatures-method	QFeatures-accessors
filename<-	QFeatures-accessors
filterFeaturesOneSE	QFeatures-filtering-oneSE
filterFeaturesOneSE,	QFeatures-filtering-oneSE
filterFeaturesOneSE,QFeatures-method	QFeatures-filtering-oneSE
findMECBlock	mv_imputation_protein
formatHSDResults	formatHSDResults
formatLimmaResult	formatLimmaResult
formatPHResults	formatPHResults
formatPHTResults	formatPHTResults
fudge2LRT	fudge2LRT
FunctionFilter	QFeatures-filtering-oneSE
FunctionFilter,	QFeatures-filtering-oneSE
FunctionFilter-class	QFeatures-filtering-oneSE
GetColorsForConditions	GetColorsForConditions
getDesignLevel	getDesignLevel
GetDetailedNbPeptides	GetDetailedNbPeptides
GetDetailedNbPeptidesUsed	GetDetailedNbPeptidesUsed
GetHistory	GetHistory
GetIndices_BasedOnConditions	GetIndices_BasedOnConditions
GetIndices_FunFiltering	GetIndices_FunFiltering
GetIndices_WholeLine	GetIndices_WholeLine
GetIndices_WholeMatrix	GetIndices_WholeMatrix
getListNbValuesInLines	getListNbValuesInLines
GetMetacellTags	QFeatures-accessors
GetMetacellTags,data.frame-method	QFeatures-accessors
GetMetacellTags,QFeatures-method	QFeatures-accessors
GetMetacellTags,SummarizedExperiment-method	QFeatures-accessors
GetMetadataSlot	QFeatures-accessors
GetNbPeptidesUsed	GetNbPeptidesUsed
GetNbTags	GetNbTags
getNumberOfEmptyLines	getNumberOfEmptyLines
getPepProtCC	getPepProtCC
getProteinsStats	getProteinsStats
getQuantile4Imp	mv_imputation_protein
GetRowdataSlot	QFeatures-accessors
GetSoftAvailables	GetSoftAvailables
GetUniqueTags	QFeatures-accessors
GetUniqueTags,QFeatures-method	QFeatures-accessors
GetUniqueTags,SummarizedExperiment-method	QFeatures-accessors
globalAdjPval	globalAdjPval
GlobalQuantileAlignment	normalization_methods
GraphPepProt	GraphPepProt
hc_logFC_DensityPlot	hc_logFC_DensityPlot
hc_mvTypePlot2	metacell-plots
heatmapForMissingValues	heatmap
histPValue_HC	histPValue_HC
HypothesisTest	QFeatures-accessors
HypothesisTest,QFeatures-method	QFeatures-accessors
HypothesisTest,SummarizedExperiment-method	QFeatures-accessors
HypothesisTest<-	QFeatures-accessors
idcol	QFeatures-accessors
idcol,QFeatures-method	QFeatures-accessors
idcol,SummarizedExperiment-method	QFeatures-accessors
idcol<-	QFeatures-accessors
imputePA2	imputePA2
InitializeHistory	InitializeHistory
innerAggregateIter	DaparToolshed-aggregate-func
innerMean	DaparToolshed-aggregate-func
innerMedian	DaparToolshed-aggregate-func
innerMedianpolish	DaparToolshed-aggregate-func
innerRobustsummary	DaparToolshed-aggregate-func
innerSum	DaparToolshed-aggregate-func
isDifferential	isDifferential
isOfType	isOfType
isSubset	isSubset
Keep_Items_from_Dataset	Keep_Items_from_Dataset
last_assay	QFeatures-utils
LH0	LH0
LH0_lm	LH0_lm
LH1	LH1
LH1_lm	LH1_lm
limmaCompleteTest	limmaCompleteTest
listSheets	output_2_Excel
LOESS	normalization_methods
mainAssay	QFeatures-accessors
makeContrast	makeContrast
makeDesign	makeDesign
makeDesign1	makeDesign1
makeDesign2	makeDesign2
makeDesign3	makeDesign3
matchMetacell	matchMetacell
MeanCentering	normalization_methods
metacell-plots	metacell-plots
metacellDef	q_metacell
MetacellFilteringScope	MetacellFilteringScope
metacellHisto_HC	metacell-plots
metacellPerLinesHistoPerCondition_HC	metacell-plots
metacellPerLinesHisto_HC	metacell-plots
metacell_agg	DaparToolshed-aggregate-func
Metacell_DIA_NN	Metacell_DIA_NN
Metacell_generic	q_metacell
Metacell_maxquant	Metacell_maxquant
Metacell_proline	Metacell_proline
metacombine	q_metacell
mvImage	metacell-plots
mv_imputation_protein	mv_imputation_protein
NAIsZero	NAIsZero
names_metacell	QFeatures-accessors
names_metacell,QFeatures-method	QFeatures-accessors
names_metacell,SummarizedExperiment-method	QFeatures-accessors
names_metacell<-	QFeatures-accessors
nEmptyLines	nEmptyLines
nonzero	nonzero
normalization_methods	normalization_methods
normalizeFunction	normalizeFunction
normalizeMethods	normalization_methods
n_assays_in_qf	QFeatures-utils
output_2_Excel	output_2_Excel
OWAnova	OWAnova
paramshistory	QFeatures-accessors
paramshistory,QFeatures-method	QFeatures-accessors
paramshistory,SummarizedExperiment-method	QFeatures-accessors
paramshistory<-	QFeatures-accessors
Parent	Parent
parentProtId	QFeatures-accessors
parentProtId,QFeatures-method	QFeatures-accessors
parentProtId,SummarizedExperiment-method	QFeatures-accessors
parentProtId<-	QFeatures-accessors
pepaTest	pepaTest
Pipelines	Pipelines
pkgsRequire	pkgsRequire
plotCompareAssays	compare-assays
plotJitter	plotJitter
plotJitter_rCharts	plotJitter_rCharts
postHocTest	postHocTest
pushpvalue	pushpvalue
QFeatures-accessors	QFeatures-accessors
QFeatures-excel	QFeatures-excel
QFeatures-filtering-oneSE	QFeatures-filtering-oneSE
QFeatures-utils	QFeatures-utils
QFeaturesFromSE	QFeatures-utils
qMetacell	QFeatures-accessors
qMetacell,QFeatures-method	QFeatures-accessors
qMetacell,SummarizedExperiment-method	QFeatures-accessors
qMetacell-filter	qMetacell-filter
qMetacell<-	QFeatures-accessors
qMetacellFilteringScope	qMetacell-filter
qMetacellOnConditions	qMetacell-filter
qMetacellWholeLine	qMetacell-filter
qMetacellWholeMatrix	qMetacell-filter
QuantileCentering	normalization_methods
q_metacell	q_metacell
readExcel	output_2_Excel
reIntroduceMEC	mv_imputation_protein
ReplaceSpecialChars	ReplaceSpecialChars
RunAggregation	RunAggregation
samLRT	samLRT
searchMetacellTags	q_metacell
select_topn	DaparToolshed-aggregate-func
separateAdjPval	separateAdjPval
SetHistory	SetHistory
Set_POV_MEC_tags	q_metacell
Set_POV_MEC_tags2	q_metacell
sharedPeptides	adjacency-matrix-filter
specPeptides	adjacency-matrix-filter
splitAdjacencyMat	splitAdjacencyMat
subAdjMat_sharedPeptides	adjacency-matrix-filter
subAdjMat_specificPeptides	adjacency-matrix-filter
subAdjMat_topnPeptides	adjacency-matrix-filter
subR25pept	subR25pept
subR25prot	subR25prot
SumByColumns	normalization_methods
SymFilteringOperators	qMetacell-filter
testAnovaModels	testAnovaModels
testDesign	testDesign
thresholdpval4fdr	thresholdpval4fdr
topnFunctions	adjacency-matrix-filter
topnPeptides	adjacency-matrix-filter
translatedRandomBeta	translatedRandomBeta
typeDataset	QFeatures-accessors
typeDataset,QFeatures-method	QFeatures-accessors
typeDataset,SummarizedExperiment-method	QFeatures-accessors
typeDataset<-	QFeatures-accessors
UpdateMetacellAfterImputation	q_metacell
UpdateMetacellAfterImputation,SummarizedExperiment-method	q_metacell
VariableFilter	QFeatures-filtering-oneSE
version	QFeatures-accessors
version,QFeatures-method	QFeatures-accessors
version<-	QFeatures-accessors
vsn	normalization_methods
wrapperCalibrationPlot	wrapperCalibrationPlot
wrapperClassic1wayAnova	wrapperClassic1wayAnova
wrapperDaparImputeMI	wrapperDaparImputeMI
wrapperImputeDetQuant	mv_imputation_protein
wrapperImputeFixedValue	mv_imputation_protein
wrapperImputeKNN	mv_imputation_protein
wrapperImputeMLE	wrapperImputeMLE
wrapperImputePA	mv_imputation_protein
wrapperImputePA2	wrapperImputePA2
wrapperImputeSLSA	mv_imputation_protein
wrapperMVImage	metacell-plots
wrapperPirat	wrapperPirat
write2excel	QFeatures-excel
write2excel,QFeatures-method	QFeatures-excel
write2excel,SummarizedExperiment-method	QFeatures-excel
write2excelSE	QFeatures-excel
writeExcel	output_2_Excel
WriteHistory	output_2_Excel
write_Assay_To_Excel	output_2_Excel
Write_RowData	output_2_Excel
Write_SamplesData_to_Excel	output_2_Excel
