IBSpectra-class         IBSpectra Class for Isobarically Tagged
                        Quantitative MS Proteomics Data
NoiseModel-class        NoiseModel objects
ProteinGroup-class      ProteinGroup objects
TlsParameter-class      Class '"TlsParameter"'
Tlsd-class              Class '"Tlsd"'
calc.delta.score        Calculate Delta Score from Ion Score
calcPeptidePosition     Recalculate peptide start positions based on
                        protein sequence
calculate.dNSAF         dNSAF approximate abundance calculations.
calculate.emPAI         emPAI approximate abundance calculations.
calculate.sample.pvalue
                        Calculate and Adjust Ratio and Sample p-values.
correct.peptide.ratios
                        Correct peptide ratios with protein ratios from
                        a separate experiment.
distrprint              Functions for distribution calculations
do.log                  Log functions for IBSpectra objects
fitCauchy               Fit weighted and unweighted Cauchy and Normal
                        distributions
getPeptideModifContext
                        Get context of modification
getPhosphoRSProbabilities
                        Generate input files for PhosphoRS, call it,
                        and get modification site probabilities
getPtmInfoFromPhosphoSitePlus
                        Get PTM site information for idenfied proteins
                        from public databases.
groupMemberPeptides     Peptide info for protein group members
human.protein.names     Info on proteins
ibspiked_set1           Isobar Data packages
isobar-analysis         IBSpectra analysis: Protein and peptide ratio
                        calculation
isobar-import           Loading data into IBSpectra objects using
                        readIBSpectra
isobar-package          Analysis and quantitation of isobarically
                        tagged MSMS proteomics data
isobar-plots            IBSpectra plots
isobar-preprocessing    IBSpectra preprocessing
isobar-reports          Isobar reports
maplot.protein          Ratio intensity plot for individual proteins
number.ranges           Helper function to transform number lists to
                        ranges
observedKnownSites      Observed modification sites.
paste0                  Isobar util functions
peptide.count           Peptide counts, spectral counts and sequence
                        coverage for ProteinGroup objects.
proteinInfo-methods     Methods for Function proteinInfo
proteinNameAndDescription
                        Get protein gene names and description from
                        protein info of protein group.
proteinRatios           Calculating and Summarizing Protein and Peptide
                        Ratios
ratiosReshapeWide       Reshape output of proteinRatios into wide
                        format
reporter.protein-methods
                        Get reporter protein group identifier for
                        protein group identifier
sanitize                Helper function for LaTeX export
shared.ratios           Shared ratio calculation
shared.ratios.sign      Plot and get significantly shared ratios.
specificities           Peptide specificities
spectra.count2          Spectral count for peptides and proteins in
                        ProteinGroup objects.
subsetIBSpectra         Subset IBSpectra objects
writeHscoreData         Write identifications into a format suitable
                        for Hscore.
writeIBSpectra          Write IBSpectra file as CSV in a format
                        readable by readIBSpectra.
