Files in CCprofiler/CCprofiler
Complex feature detection using SEC protein chromatograms.
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/.Rapp.history
R/._CreateGroupsFromNetworkTable.R
R/._annotateComplexFeatures.R
R/._annotateTraces.R
R/._calculateFeatureCorrelation.R
R/._calculateSibPepCorr.R
R/._calibrateSECMW.R
R/._collapseComplexFearures.R
R/._complexFeaturesMethods.R
R/._desertedFunctions.R
R/._estimateComplexFeatureStoichiometry.R
R/._extractIdsFromFastaHeader.R
R/._filterBySibPepCorr.R
R/._filterConsecutiveIdStretches.R
R/._findComplexFeatures.R
R/._findComplexFeaturesPP.R
R/._findFeaturePeaks.R
R/._findProteinFeatures.R
R/._generateHypotheses.R
R/._importFromOpenSWATH.R
R/._proteinQuantification.R
R/._runSECexplorer.R
R/._tracesMethods.R
R/annotateComplexFeatures.R
R/annotateMassDistribution.R
R/annotateTraces.R
R/calculateFeatureCorrelation.R
R/calculateSibPepCorr.R
R/calibrateMW.R
R/collapseComplexFearures.R
R/collapseHypothesisWideFeatures.R
R/complexFeatureGridSearch.R
R/complexFeatureMethods.R
R/data.R
R/estimateComplexFeatureStoichiometry.R
R/estimateQvalues.R
R/featureFDRestimation.R
R/featureMethods.R
R/filterBySibPepCorr.R
R/filterConsecutiveIdStretches.R
R/findComplexFeatures.R
R/findComplexFeaturesPP.R
R/findComplexFeaturesSW.R
R/findProteinFeatures.R
R/generateHypotheses.R
R/generateHypothesesHelpers.R
R/getBestFeatureParameters.R
R/importFromOpenSWATH.R
R/importPCPdata.R
R/imputeMissingValues.R
R/plotFeatures.R
R/plotSibPepCorrDensities.R
R/plotSummarizedMScoverage.R
R/plottingHelpers.R
R/proteinFeatureGridSearch.R
R/proteinQuantification.R
R/proteoformAnnotation.R
R/rocSibPepCorr.R
R/runSECexplorer.R
R/tracesMethods.R
README.md
SECprofiler.Rproj
data/.Rapp.history
data/corumComplexHypotheses.rda
data/corumComplexHypothesesRedundant.rda
data/exampleCalibrationTable.rda
data/exampleComplexFeatures.rda
data/exampleComplexHypotheses.rda
data/exampleFractionAnnotation.rda
data/exampleOpenSWATHinput.rda
data/examplePCPdataLong.rda
data/examplePCPdataWide.rda
data/examplePeptideTraces.rda
data/examplePeptideTracesFiltered.rda
data/examplePeptideTracesUnannotated.rda
data/exampleProteinFeatures.rda
data/exampleProteinTraces.rda
data/exampleTraceAnnotation.rda
data/fullProtTracesHEK.rda
data/uniprotNameAnnotated.rda
developer_guidelines.md
inst/citations.bib
install_r_packages
man/SECexplorer_processing.Rd
man/annotateComplexFeatures.Rd
man/annotateMassDistribution.Rd
man/annotateMolecularWeight.Rd
man/annotateTraces.Rd
man/appendSecondaryComplexFeatures.Rd
man/calculateCoelutionScore.Rd
man/calculateFeatureCorrelation.Rd
man/calculatePathlength.Rd
man/calculateQvalue.Rd
man/calculateSibPepCorr.Rd
man/calibrateMW.Rd
man/callapseByUniqueFeatureGroups.Rd
man/collapseComplexFeatures.Rd
man/collapseHypothesis.Rd
man/complexClustering.Rd
man/convertIDs.Rd
man/corumComplexHypotheses.Rd
man/corumComplexHypothesesRedundant.Rd
man/createGGplotColMap.Rd
man/dot-collapseWideHypothesis.Rd
man/dot-tracesTest.Rd
man/estimateComplexFeatureStoichiometry.Rd
man/estimateDecoyFDR.Rd
man/estimateGridSearchDecoyFDR.Rd
man/exampleCalibrationTable.Rd
man/exampleComplexFeatures.Rd
man/exampleComplexHypotheses.Rd
man/exampleFractionAnnotation.Rd
man/exampleOpenSWATHinput.Rd
man/examplePCPdataLong.Rd
man/examplePCPdataWide.Rd
man/examplePeptideTraces.Rd
man/examplePeptideTracesFiltered.Rd
man/examplePeptideTracesUnannotated.Rd
man/exampleProteinFeatures.Rd
man/exampleProteinTraces.Rd
man/exampleTraceAnnotation.Rd
man/filterByMaxCorr.Rd
man/filterBySibPepCorr.Rd
man/filterByStepwiseCompleteness.Rd
man/filterConsecutiveIdStretches.Rd
man/filterFeatures.Rd
man/filterGridSearchResults.Rd
man/findComplexFeatures.Rd
man/findComplexFeaturesPP.Rd
man/findComplexFeaturesSW.Rd
man/findComplexFeaturesWithinWindow.Rd
man/findFeatureBoundaries.Rd
man/findMissingValues.Rd
man/findProteinFeatures.Rd
man/generateBinaryNetwork.Rd
man/generateComplexDecoys.Rd
man/generateComplexTargets.Rd
man/generateDecoys.Rd
man/generateRandomPepTraces.Rd
man/getBestFeatures.Rd
man/getBestParameterData.Rd
man/getBestParameterStats.Rd
man/getBestParameterStats_constraintFDR.Rd
man/getBestQvalueParameters.Rd
man/getDistance.Rd
man/getDistanceMatrix.Rd
man/getGenePepList.Rd
man/getIntensityMatrix.Rd
man/getUniqueFeatureGroups.Rd
man/importFromOpenSWATH.Rd
man/importPCPdata.Rd
man/imputeMissingVals.Rd
man/imputeMissingValues.Rd
man/imputeTraces.Rd
man/performComplexGridSearch.Rd
man/performProteinGridSearch.Rd
man/plot.traces.Rd
man/plotComplexCompletenessScatter.Rd
man/plotComplexMScoveragePie.Rd
man/plotComplexMScoverageScatter.Rd
man/plotFeatures.Rd
man/plotIdFDRspace.Rd
man/plotImputationSummary.Rd
man/plotProteinMScoveragePie.Rd
man/plotScoreDistribution.Rd
man/plotSibPepCorrDensities.Rd
man/plotSummarizedComplexes.Rd
man/plotSummarizedMScoverage.Rd
man/proteinQuantification.Rd
man/qvaluePositivesPlot.Rd
man/qvaluePositivesPlotGrid.Rd
man/rocSibPepCorr.Rd
man/runSECexplorer.Rd
man/runSlidingWindow.Rd
man/scoreFeatures.Rd
man/subset.traces.Rd
man/summarizeFeatures.Rd
man/summarizeMassDistribution.Rd
man/summary.traces.Rd
man/toLongFormat.Rd
tests/testthat.R
tests/testthat/test_SibPepCorr.R
tests/testthat/test_annotateTraces.R
tests/testthat/test_calibrateMW.R
tests/testthat/test_collapseHypothesisWideFeatures.R
tests/testthat/test_complexFeatureGridSearch.R
tests/testthat/test_featureMethods.R
tests/testthat/test_filterConsecutiveIdStretches.R
tests/testthat/test_findComplexFeatures.R
tests/testthat/test_generateHypotheses.R
tests/testthat/test_getBestFeatureParameters.R
tests/testthat/test_importFromOpenSWATH.R
tests/testthat/test_importPCPdata.R
tests/testthat/test_proteinFeatureGridSearch.R
tests/testthat/test_proteinQuantification.R
tests/testthat/test_tracesMethods.R
vignettes/CCprofiler_vignette.Rmd
