.checkContrastMatrix	dot-checkContrastMatrix
.checkSummarizationParams	dot-checkSummarizationParams
.countRunsWithNorm	dot-countRunsWithNorm
.documentFunction	dot-documentFunction
.getNormalizationAbundance	dot-getNormalizationAbundance
.getRunsMedian	dot-getRunsMedian
.handleSingleContrastTMT	dot-handleSingleContrastTMT
.logSum	dot-logSum
.logSummarizationParams	dot-logSummarizationParams
.makeContrastSingleTMT	dot-makeContrastSingleTMT
.makeFactorColumnsTMT	dot-makeFactorColumnsTMT
.medianPolish	dot-medianPolish
.normalizePeptides	dot-normalizePeptides
.normalizeProteins	dot-normalizeProteins
.prepareForSummarization	dot-prepareForSummarization
.removeRedundantChannels	dot-removeRedundantChannels
.summarizeMSstats	dot-summarizeMSstats
.summarizeSimpleStat	dot-summarizeSimpleStat
.summarizeTMP	dot-summarizeTMP
.summarizeTMT	dot-summarizeTMT
annotation.mine	annotation.mine
annotation.mq	annotation.mq
annotation.pd	annotation.pd
dataProcessPlotsTMT	dataProcessPlotsTMT
evidence	evidence
getProcessedTMT	getProcessedTMT
getSummarizedTMT	getSummarizedTMT
groupComparisonTMT	groupComparisonTMT
input.pd	input.pd
MaxQtoMSstatsTMTFormat	MaxQtoMSstatsTMTFormat
MSstatsComparisonModelSingleTMT	MSstatsComparisonModelSingleTMT
MSstatsFitComparisonModelsTMT	MSstatsFitComparisonModelsTMT
MSstatsGroupComparisonOutputTMT	MSstatsGroupComparisonOutputTMT
MSstatsGroupComparisonTMT	MSstatsGroupComparisonTMT
MSstatsModerateTTest	MSstatsModerateTTest
MSstatsNormalizeTMT	MSstatsNormalizeTMT
MSstatsPrepareForGroupComparisonTMT	MSstatsPrepareForGroupComparisonTMT
MSstatsPrepareForSummarizationTMT	MSstatsPrepareForSummarizationTMT
MSstatsSummarizationOutputTMT	MSstatsSummarizationOutputTMT
MSstatsSummarizeTMT	MSstatsSummarizeTMT
MSstatsTestSingleProteinTMT	MSstatsTestSingleProteinTMT
MSstatsTMT	MSstatsTMT
OpenMStoMSstatsTMTFormat	OpenMStoMSstatsTMTFormat
PDtoMSstatsTMTFormat	PDtoMSstatsTMTFormat
PhilosophertoMSstatsTMTFormat	PhilosophertoMSstatsTMTFormat
proteinGroups	proteinGroups
proteinSummarization	proteinSummarization
quant.pd.msstats	quant.pd.msstats
raw.mine	raw.mine
raw.om	raw.om
raw.pd	raw.pd
SpectroMinetoMSstatsTMTFormat	SpectroMinetoMSstatsTMTFormat
test.pairwise	test.pairwise
