Files in Vitek-Lab/MSstatsTMT
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
MSstatsTMT.Rproj
NAMESPACE
R/converters.R
R/dataProcessPlotsTMT.R
R/designSampleSizeTMT.R
R/groupComparisonTMT.R
R/proteinSummarization.R
R/utils_MSstatsTMT.R
R/utils_group_comparison.R
R/utils_summarization_checks.R
R/utils_summarization_methods.R
R/utils_summarization_normalize.R
README.md
codecov.yml
data/annotation.mine.rda
data/annotation.mq.rda
data/annotation.pd.rda
data/datalist
data/evidence.rda
data/input.pd.rda
data/proteinGroups.rda
data/quant.pd.msstats.rda
data/raw.mine.rda
data/raw.om.rda
data/raw.pd.rda
data/test.pairwise.rda
inst/.DS_Store
inst/CITATION
inst/NEWS.Rd
man/MSstatsComparisonModelSingleTMT.Rd
man/MSstatsFitComparisonModelsTMT.Rd
man/MSstatsGroupComparisonOutputTMT.Rd
man/MSstatsGroupComparisonTMT.Rd
man/MSstatsModerateTTest.Rd
man/MSstatsNormalizeTMT.Rd
man/MSstatsPrepareForGroupComparisonTMT.Rd
man/MSstatsPrepareForSummarizationTMT.Rd
man/MSstatsSummarizationOutputTMT.Rd
man/MSstatsSummarizeTMT.Rd
man/MSstatsTMT.Rd
man/MSstatsTestSingleProteinTMT.Rd
man/MaxQtoMSstatsTMTFormat.Rd
man/OpenMStoMSstatsTMTFormat.Rd
man/PDtoMSstatsTMTFormat.Rd
man/PhilosophertoMSstatsTMTFormat.Rd
man/SpectroMinetoMSstatsTMTFormat.Rd
man/annotation.mine.Rd
man/annotation.mq.Rd
man/annotation.pd.Rd
man/dataProcessPlotsTMT.Rd
man/designSampleSizeTMT.Rd
man/dot-calculatePower.Rd
man/dot-checkContrastMatrix.Rd
man/dot-checkSummarizationParams.Rd
man/dot-countRunsWithNorm.Rd
man/dot-documentFunction.Rd
man/dot-getMedianSigmaRun.Rd
man/dot-getMedianSigmaSubject.Rd
man/dot-getNormalizationAbundance.Rd
man/dot-getNumSample.Rd
man/dot-getPhilosopherInput.Rd
man/dot-getRunsMedian.Rd
man/dot-getVarComponentTMT.Rd
man/dot-handleSingleContrastTMT.Rd
man/dot-logSum.Rd
man/dot-logSummarizationParams.Rd
man/dot-makeContrastSingleTMT.Rd
man/dot-makeFactorColumnsTMT.Rd
man/dot-medianPolish.Rd
man/dot-normalizePeptides.Rd
man/dot-normalizeProteins.Rd
man/dot-prepareForSummarization.Rd
man/dot-removeRedundantChannels.Rd
man/dot-summarizeMSstats.Rd
man/dot-summarizeSimpleStat.Rd
man/dot-summarizeTMP.Rd
man/dot-summarizeTMT.Rd
man/evidence.Rd
man/getProcessedTMT.Rd
man/getSummarizedTMT.Rd
man/groupComparisonTMT.Rd
man/input.pd.Rd
man/proteinGroups.Rd
man/proteinSummarization.Rd
man/quant.pd.msstats.Rd
man/raw.mine.Rd
man/raw.om.Rd
man/raw.pd.Rd
man/test.pairwise.Rd
tests/testthat.R
tests/testthat/test-PDtoMSstatsTMTFormat.R
tests/testthat/test-groupComparisionTMT.R
tests/testthat/test-proteinSummarization.R
vignettes/MSstatsTMT.Rmd
