pulsedSilac
Analysis of pulsed-SILAC quantitative proteomics data

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Functions
229
Source code
85
Man pages
31
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pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data
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API

API for pulsedSilac
Analysis of pulsed-SILAC quantitative proteomics data

Global functions
$,SilacProteomicsExperiment-method Man page
$<-,SilacProteomicsExperiment-method Man page
.SilacPeptideExperiment Man page
.SilacProteinExperiment Man page
.SilacProteomicsExperiment Man page
.compareAIC Source code
.giveMetaoption Source code
.loopWrapper Source code
.modelTurnover Source code
.plotCompareModel.Assay Source code
.plotCompareModel.Model Source code
.plotCompareModel.Parameter Source code
.plotDistributionModel.Assay Source code
.plotDistributionModel.Model Source code
.plotDistributionModel.Parameter Source code
.processColDataPlot Source code
.removeDuplicatesMetaoptions Source code
.valid.SilacPeptideExperiment Source code
.valid.SilacPeptideExperiment.colData Source code
.valid.SilacPeptideExperiment.metaoptions Source code
.valid.SilacPeptideExperiment.rowData Source code
.valid.SilacProteinExperiment Source code
.valid.SilacProteinExperiment.colData Source code
.valid.SilacProteinExperiment.metaoptions Source code
.valid.SilacProteinExperiment.rowData Source code
.valid.SilacProteomicsExperiment Source code
.valid.SilacProteomicsExperiment.colData Source code
.valid.SilacProteomicsExperiment.linkerDf Source code
.valid.SilacProteomicsExperiment.metaoptions Source code
.valid.SilacProteomicsExperiment.ncol Source code
PeptExp Man page Source code
ProtExp Man page Source code
SilacPeptideExperiment Man page Source code
SilacPeptideExperiment-class Man page
SilacPeptideExperiment-constructor Man page
SilacProteinExperiment Man page Source code
SilacProteinExperiment-class Man page
SilacProteinExperiment-constructor Man page
SilacProteinPeptideExperiment-accessors Man page
SilacProteomicsExperiment Man page Source code
SilacProteomicsExperiment-accessors Man page
SilacProteomicsExperiment-class Man page
SilacProteomicsExperiment-constructor Man page
[,SilacProteomicsExperiment,ANY,ANY,ANY-method Man page
[,SilacProteomicsExperiment-ANY-ANY-method Man page
addMisscleavedPeptides Man page
addMisscleavedPeptides,SilacPeptideExperiment-method Man page
addMisscleavedPeptides,SilacProteinExperiment-method Man page
addMisscleavedPeptides,SilacProteomicsExperiment-method Man page
assayNames,SilacProteomicsExperiment-method Man page
assayNamesPept Man page
assayNamesPept,SilacPeptideExperiment-method Man page
assayNamesPept,SilacProteomicsExperiment-method Man page
assayNamesPept<- Man page
assayNamesPept<-,SilacPeptideExperiment-method Man page
assayNamesPept<-,SilacProteomicsExperiment-method Man page
assayNamesProt Man page
assayNamesProt,SilacProteinExperiment-method Man page
assayNamesProt,SilacProteomicsExperiment-method Man page
assayNamesProt<- Man page
assayNamesProt<-,SilacProteinExperiment-method Man page
assayNamesProt<-,SilacProteomicsExperiment-method Man page
assays Man page
assays,SilacProteomicsExperiment-method Man page
assays<-,SilacPeptideExperiment,ANY-method Man page
assays<-,SilacProteinExperiment,ANY-method Man page
assaysPept Man page
assaysPept,SilacPeptideExperiment-method Man page
assaysPept,SilacProteomicsExperiment-method Man page
assaysPept<- Man page
assaysPept<-,SilacPeptideExperiment-method Man page
assaysPept<-,SilacProteomicsExperiment-method Man page
assaysProt Man page
assaysProt,SilacProteinExperiment-method Man page
assaysProt,SilacProteomicsExperiment-method Man page
assaysProt<- Man page
assaysProt<-,SilacProteinExperiment-method Man page
assaysProt<-,SilacProteomicsExperiment-method Man page
barplotCounts Man page
barplotCounts,SilacPeptideExperiment-method Man page
barplotCounts,SilacProteinExperiment-method Man page
barplotCounts,SilacProteomicsExperiment-method Man page
barplotTimeCoverage Man page
barplotTimeCoverage,SilacPeptideExperiment-method Man page
barplotTimeCoverage,SilacProteinExperiment-method Man page
barplotTimeCoverage,SilacProteomicsExperiment-method Man page
buildLinkerDf Man page Source code
calculateAIC Man page Source code
calculateIsotopeFraction Man page
calculateIsotopeFraction,SilacPeptideExperiment-method Man page
calculateIsotopeFraction,SilacProteinExperiment-method Man page
calculateIsotopeFraction,SilacProteomicsExperiment-method Man page
calculateIsotopeRatio Man page
calculateIsotopeRatio,SilacPeptideExperiment-method Man page
calculateIsotopeRatio,SilacProteinExperiment-method Man page
calculateIsotopeRatio,SilacProteomicsExperiment-method Man page
calculateOldIsotopePool Man page
calculateOldIsotopePool,SilacPeptideExperiment-method Man page
calculateOldIsotopePool,SilacProteomicsExperiment-method Man page
cbind,SilacPeptideExperiment-method Man page
cbind,SilacProteinExperiment-method Man page
cbind,SilacProteomicsExperiment-method Man page
checkLinkerDf Source code
coerce Man page
coerce,SilacProteinExperiment,SummarizedExperiment-method Man page
coerce,SilacProteinExperiment,data.frame-method Man page
colData,SilacProteomicsExperiment-method Man page
colData<-,SilacPeptideExperiment,ANY-method Man page
colData<-,SilacPeptideExperiment-method Man page
colData<-,SilacProteinExperiment,ANY-method Man page
colData<-,SilacProteinExperiment-method Man page
colData<-,SilacProteomicsExperiment,ANY-method Man page
colData<-,SilacProteomicsExperiment-method Man page
colnames,SilacProteomicsExperiment-method Man page
colnames<-,SilacProteomicsExperiment-method Man page
compareAIC Man page Source code
compareOptions Source code
dim,SilacProteomicsExperiment-method Man page
filterByMissingTimepoints Man page
filterByMissingTimepoints,SilacPeptideExperiment-method Man page
filterByMissingTimepoints,SilacProteinExperiment-method Man page
filterByMissingTimepoints,SilacProteomicsExperiment-method Man page
hasAssayNames Source code
hasMetaoption Source code
length,SilacProteomicsExperiment-method Man page
linkerDf Man page
linkerDf,SilacProteomicsExperiment-method Man page
linkerDf<- Man page
linkerDf<-,SilacProteomicsExperiment-method Man page
mefPE Man page
merge Man page
merge,SilacPeptideExperiment,ANY-method Man page
merge,SilacProteinExperiment,ANY-method Man page
merge,SilacProteomicsExperiment,ANY-method Man page
mergeMetaoptions Source code
mergeModelsLists Man page Source code
metadata,SilacProteomicsExperiment-method Man page
metadata<-,SilacProteomicsExperiment-method Man page
metaoptionInColData Source code
metaoptionInRowData Source code
metaoptions Man page
metaoptions,SilacPeptideExperiment-method Man page
metaoptions,SilacProteinExperiment-method Man page
metaoptions,SilacProteomicsExperiment-method Man page
metaoptions<- Man page
metaoptions<-,SilacPeptideExperiment-method Man page
metaoptions<-,SilacProteinExperiment-method Man page
metaoptions<-,SilacProteomicsExperiment-method Man page
modelTurnover Man page
modelTurnover,SilacPeptideExperiment-method Man page
modelTurnover,SilacProteinExperiment-method Man page
modelTurnover,SilacProteomicsExperiment-method Man page
mostStable Man page
mostStable,SilacPeptideExperiment-method Man page
mostStable,SilacProteinExperiment-method Man page
mostStable,SilacProteomicsExperiment-method Man page
ncol Man page
ncol,SilacProteomicsExperiment-method Man page
nrow,SilacProteomicsExperiment-method Man page
plotDistributionAssay Man page
plotDistributionAssay,SilacPeptideExperiment-method Man page
plotDistributionAssay,SilacProteinExperiment-method Man page
plotDistributionAssay,SilacProteomicsExperiment-method Man page
plotDistributionModel Man page Source code
plotIndividualModel Man page
plotIndividualModel,SilacPeptideExperiment-method Man page
plotIndividualModel,SilacProteinExperiment-method Man page
plotIndividualModel,SilacProteomicsExperiment-method Man page
rbind,SilacPeptideExperiment-method Man page
rbind,SilacProteinExperiment-method Man page
rbind,SilacProteomicsExperiment-method Man page
rbindLinkerDf Source code
recycleLightLysine Man page
rowData,SilacProteomicsExperiment-method Man page
rowData<-,SilacPeptideExperiment-method Man page
rowData<-,SilacProteinExperiment-method Man page
rowData<-,SilacProteomicsExperiment-method Man page
rowDataPept Man page
rowDataPept,SilacPeptideExperiment-method Man page
rowDataPept,SilacProteomicsExperiment-method Man page
rowDataPept<- Man page
rowDataPept<-,SilacPeptideExperiment-method Man page
rowDataPept<-,SilacProteomicsExperiment-method Man page
rowDataProt Man page
rowDataProt,SilacProteinExperiment-method Man page
rowDataProt,SilacProteomicsExperiment-method Man page
rowDataProt<- Man page
rowDataProt<-,SilacProteinExperiment-method Man page
rowDataProt<-,SilacProteomicsExperiment-method Man page
rownamesPept Man page
rownamesPept,SilacProteomicsExperiment-method Man page
rownamesPept<- Man page
rownamesPept<-,SilacProteomicsExperiment-method Man page
rownamesProt Man page
rownamesProt,SilacProteomicsExperiment-method Man page
rownamesProt<- Man page
rownamesProt<-,SilacProteomicsExperiment-method Man page
scatterCompareAssays Man page
scatterCompareAssays,SilacPeptideExperiment-method Man page
scatterCompareAssays,SilacProteinExperiment-method Man page
scatterCompareAssays,SilacProteomicsExperiment-method Man page
scatterCompareModels Man page Source code
subset,SilacPeptideExperiment-method Man page
subset,SilacProteinExperiment-method Man page
subset,SilacProteomicsExperiment-method Man page
subsetLinkerDf Source code
subsetPept Man page
subsetPept,SilacPeptideExperiment-method Man page
subsetPept,SilacProteomicsExperiment-method Man page
subsetProt Man page
subsetProt,SilacProteinExperiment-method Man page
subsetProt,SilacProteomicsExperiment-method Man page
synchronizeMetaoptions Source code
upsetTimeCoverage Man page
upsetTimeCoverage,SilacPeptideExperiment-method Man page
upsetTimeCoverage,SilacProteinExperiment-method Man page
upsetTimeCoverage,SilacProteomicsExperiment-method Man page
wormsPE Man page
pulsedSilac documentation built on Nov. 8, 2020, 5:13 p.m.

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