isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.

AuthorFlorian P Breitwieser <florian.bw@gmail.com> and Jacques Colinge <jacques.colinge@inserm.fr>, with contributions from Alexey Stukalov <stukalov@biochem.mpg.de>, Xavier Robin <xavier.robin@unige.ch> and Florent Gluck <florent.gluck@unige.ch>
Date of publicationNone
MaintainerFlorian P Breitwieser <florian.bw@gmail.com>
LicenseLGPL-2
Version1.20.0
https://github.com/fbreitwieser/isobar

View on Bioconductor

Man pages

calc.delta.score: Calculate Delta Score from Ion Score

calc.startpos: Recalculate peptide start positions based on protein sequence

calculate.dNSAF: dNSAF approximate abundance calculations.

calculate.emPAI: emPAI approximate abundance calculations.

calculate-pvalues: Calculate and Adjust Ratio and Sample p-values.

correct.peptide.ratios: Correct peptide ratios with protein ratios from a separate...

distr-methods: Functions for distribution calculations

fit-distr: Fit weighted and unweighted Cauchy and Normal distributions

getPeptideModifContext: Get context of modification

getPhosphoRSProbabilities: Generate input files for PhosphoRS, call it, and get...

getPtmInfo: Get PTM site information for idenfied proteins from public...

groupMemberPeptides: Peptide info for protein group members

human.protein.names: Info on proteins

IBSpectra-class: IBSpectra Class for Isobarically Tagged Quantitative MS...

isobar-analysis: IBSpectra analysis: Protein and peptide ratio calculation

isobar-data: Isobar Data packages

isobar-import: Loading data into IBSpectra objects using readIBSpectra

isobar-log: Log functions for IBSpectra objects

isobar-package: Analysis and quantitation of isobarically tagged MSMS...

isobar-plots: IBSpectra plots

isobar-preprocessing: IBSpectra preprocessing

isobar-reports: Isobar reports

maplot.protein: Ratio intensity plot for individual proteins

NoiseModel-class: NoiseModel objects

number.ranges: Helper function to transform number lists to ranges

observedKnownSites: Observed modification sites.

peptide.count: Peptide counts, spectral counts and sequence coverage for...

ProteinGroup-class: ProteinGroup objects

proteinInfo-methods: Methods for Function proteinInfo

proteinNameAndDescription: Get protein gene names and description from protein info of...

ratiosReshapeWide: Reshape output of proteinRatios into wide format

ratio-summ: Calculating and Summarizing Protein and Peptide Ratios

reporter.protein-methods: Get reporter protein group identifier for protein group...

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...

subsetIBSpectra: Subset IBSpectra objects

Tlsd-class: Class '"Tlsd"'

TlsParameter-class: Class '"TlsParameter"'

utils: Isobar util functions

writeHscoreData: Write identifications into a format suitable for Hscore.

writeIBSpectra: Write IBSpectra file as CSV in a format readable by...

Functions

AbscontDistribution-class Man page
adjust.ratio.pvalue Man page
as.data.frame.IBSpectra Man page
as.data.frame,IBSpectra-method Man page
as.data.frame.ProteinGroup Man page
as.data.frame,ProteinGroup-method Man page
calcCumulativeProbXGreaterThanY Man page
calc.delta.score Man page
calc.pep.delta.score Man page
calcPeptidePosition Man page
calcProbXDiffNormals Man page
calcProbXGreaterThanY Man page
calculate.dNSAF Man page
calculate.emPAI Man page
calculate.mult.sample.pvalue Man page
calculate.ratio.pvalue Man page
calculate.sample.pvalue Man page
class:IBSpectra Man page
classLabels Man page
classLabels<- Man page
classLabels<-,IBSpectra-method Man page
classLabels,IBSpectra-method Man page
class:NoiseModel Man page
class:ProteinGroup Man page
coerce,data.frame,ProteinGroup-method Man page
coerce,IBSpectra,data.frame-method Man page
combn.matrix Man page
combn.protein.tbl Man page
connect.nodes Man page
correctIsotopeImpurities Man page
correctIsotopeImpurities,IBSpectra-method Man page
correct.peptide.ratios Man page
create.meta.reports Man page
create.reports Man page
Distribution-class Man page
distrprint Man page
do.log Man page
do.log,IBSpectra,character-method Man page
draw.boxplot Man page
draw.protein.group Man page
draw.proteingroup.row Man page
estimateRatio Man page
estimateRatioForPeptide Man page
estimateRatioForProtein Man page
estimateRatio,IBSpectra,ANY,character,character,character,missin Man page
estimateRatio,IBSpectra,ANY,character,character,character,NULL-m Man page
estimateRatio,IBSpectra,ANY,character,character,missing,characte Man page
estimateRatio,IBSpectra,ANY,character,character,missing,data.fra Man page
estimateRatio,IBSpectra,ANY,character,character,missing,matrix-m Man page
estimateRatio,IBSpectra,ANY,character,character,NULL,character-m Man page
estimateRatio,IBSpectra,ANY,character,character,NULL,data.frame- Man page
estimateRatio,IBSpectra,ANY,character,character,NULL,matrix-meth Man page
estimateRatio,IBSpectra,ANY,missing,missing,character,missing-me Man page
estimateRatio,IBSpectra,ANY,missing,missing,missing,character-me Man page
estimateRatioNumeric Man page
estimateRatioNumeric,numeric,numeric,missing-method Man page
estimateRatioNumeric,numeric,numeric,NoiseModel-method Man page
estimateRatioNumeric,numeric,numeric,NULL-method Man page
exclude Man page
exclude,IBSpectra,character-method Man page
ExponentialNoANoiseModel-class Man page
ExponentialNoiseModel-class Man page
filterSpectraDeltaScore Man page
filterSpectraPhosphoRS Man page
fitCauchy Man page
fitGaussianMixture Man page
fitNorm Man page
fitNormalCauchyMixture Man page
fitTlsd Man page
fitWeightedNorm Man page
GeneralNoiseModel-class Man page
get.log Man page
get.log,IBSpectra,character-method Man page
getMultUnifDensity Man page
getMultUnifPValues Man page
get_n_proteins Man page
get.pep.group Man page
getPeptideModifContext Man page
getPhosphoRSProbabilities Man page
getProteinInfoFromBioDb Man page
getProteinInfoFromBiomart Man page
getProteinInfoFromEntrez Man page
getProteinInfoFromNextProt Man page
getProteinInfoFromTheInternet Man page
getProteinInfoFromUniprot Man page
getPtmInfoFromNextprot Man page
getPtmInfoFromPhosphoSitePlus Man page
groupMemberPeptides Man page
group-specific Man page
GROUPSPECIFIC Man page
human.protein.names Man page
ib_phospho Man page
IBSpectra Man page
ibSpectra.as.concise.data.frame Man page
IBSpectra-class Man page
IBSpectraTypes Man page
ibspiked_set1 Man page
ibspiked_set2 Man page
indistinguishableProteins Man page
indistinguishableProteins,ProteinGroup,ANY,ANY-method Man page
indistinguishableProteins,ProteinGroup,character,missing-method Man page
indistinguishableProteins,ProteinGroup-method Man page
indistinguishableProteins,ProteinGroup,missing,character-method Man page
indistinguishableProteins,ProteinGroup,missing,missing-method Man page
initialize.env Man page
initialize,IBSpectra-method Man page
initialize,NoiseModel-method Man page
\%inrange\% Man page
InverseNoANoiseModel-class Man page
InverseNoiseModel-class Man page
is.logged Man page
is.logged,IBSpectra,character-method Man page
isobar Man page
isobar-analysis Man page
isobar-import Man page
isobar-package Man page
isobar-plots Man page
isobar-preprocessing Man page
isobar-reports Man page
isotopeImpurities Man page
isotopeImpurities<- Man page
isotopeImpurities<-,IBSpectra-method Man page
isotopeImpurities,IBSpectra-method Man page
iTRAQ4plexSpectra Man page
iTRAQ4plexSpectra-class Man page
iTRAQ8plexSpectra Man page
iTRAQ8plexSpectra-class Man page
iTRAQSpectra Man page
iTRAQSpectra-class Man page
load.properties Man page
load.tex.properties Man page
lowIntensity Man page
lowIntensity<- Man page
lowIntensity<-,NoiseModel-method Man page
lowIntensity,NoiseModel-method Man page
maplot Man page
maplot2 Man page
maplot2,ANY,character,character-method Man page
maplot2,list,character,character-method Man page
maplot,IBSpectra,character,character-method Man page
maplot,IBSpectra,missing,missing-method Man page
maplot,missing,numeric,numeric-method Man page
maplot.protein Man page
modifs Man page
modif.site.count Man page
modif.sites Man page
my.protein.info Man page
naRegion Man page
naRegion<- Man page
naRegion<-,NoiseModel-method Man page
naRegion,NoiseModel-method Man page
n.observable.peptides Man page
noiseFunction Man page
noiseFunction,NoiseModel-method Man page
NoiseModel Man page
NoiseModel-class Man page
noise.model.hcd Man page
NoiseModel,IBSpectra-method Man page
normalize Man page
normalize,IBSpectra-method Man page
number.ranges Man page
observable.peptides Man page
observedKnownSites Man page
parameter Man page
parameter<- Man page
Parameter-class Man page
parameter<-,NoiseModel-method Man page
parameter,NoiseModel-method Man page
paste0 Man page
peptide.count Man page
peptideInfo Man page
peptideInfo-methods Man page
peptideInfo,ProteinGroup-method Man page
peptideNProtein Man page
peptideNProtein,ProteinGroup-method Man page
peptideRatios Man page
peptideRatiosNotQuant Man page
peptides Man page
peptideSpecificity Man page
peptideSpecificity Man page
peptideSpecificity,ProteinGroup-method Man page
peptideSpecificity,ProteinGroup-method Man page
peptides,ProteinGroup,character-method Man page
peptides,ProteinGroup,missing-method Man page
plot.NoiseModel Man page
plotRatio Man page
plotRatio,IBSpectra,character,character,character-method Man page
print_classlabels_tbl Man page
print_groupsize Man page
print_longtablehdr Man page
print_longtablehdr_peptide Man page
print_protein_grp_info Man page
print_protein_grp_tbl Man page
print_protein_notquant_tbl Man page
print_protein_quant_tbl Man page
print_sign_proteins_tbl Man page
property Man page
protein.ac Man page
protein.ac,ProteinGroup,character-method Man page
protein.ac,ProteinGroup,missing-method Man page
proteinDescription Man page
protein.g Man page
proteinGeneName Man page
protein.g,ProteinGroup,character,character-method Man page
protein.g,ProteinGroup,character-method Man page
proteinGroup Man page
proteinGroup<- Man page
ProteinGroup Man page
ProteinGroup Man page
proteinGroup.as.concise.data.frame Man page
ProteinGroup-class Man page
ProteinGroup,data.frame,missing-method Man page
ProteinGroup,data.frame,NULL-method Man page
ProteinGroup,data.frame,ProteinGroup-method Man page
proteinGroup<-,IBSpectra-method Man page
proteinGroup,IBSpectra-method Man page
proteinGroupTable Man page
proteinGroupTable,ProteinGroup-method Man page
proteinID Man page
proteinInfo Man page
proteinInfo<- Man page
proteinInfoIsOnSpliceVariants Man page
proteinInfo-methods Man page
proteinInfo,ProteinGroup,character,missing-method Man page
proteinInfo<-,ProteinGroup-method Man page
proteinInfo,ProteinGroup-method Man page
proteinInfo,ProteinGroup,missing,character-method Man page
proteinInfo,ProteinGroup,missing,missing-method Man page
proteinNameAndDescription Man page
proteinRatios Man page
protGgdata Man page
protGgdata,ANY,character,character-method Man page
raplot Man page
raplot,IBSpectra-method Man page
ratiosReshapeWide Man page
readIBSpectra Man page
readIBSpectra,character,character,character-method Man page
readIBSpectra,character,character-method Man page
readIBSpectra,character,character,missing-method Man page
readIBSpectra,character,data.frame,character-method Man page
readIBSpectra,character,data.frame,missing-method Man page
read.mzid Man page
readPhosphoRSOutput Man page
readProteinGroup Man page
readProteinGroup2 Man page
reporterData Man page
reporterData<- Man page
reporterData<-,IBSpectra-method Man page
reporterData,IBSpectra-method Man page
reporterIntensities Man page
reporterIntensities<- Man page
reporterIntensities<-,IBSpectra-method Man page
reporterIntensities,IBSpectra-method Man page
reporterIntensityPlot Man page
reporterIntensityPlot,IBSpectra-method Man page
reporterIntensityPlot-methods Man page
reporterMasses Man page
reporterMasses<- Man page
reporterMasses<-,IBSpectra-method Man page
reporterMasses,IBSpectra-method Man page
reporterMassPrecision Man page
reporterMassPrecision,IBSpectra,logical-method Man page
reporterMassPrecision,IBSpectra,missing-method Man page
reporter.protein Man page
reporter.protein-methods Man page
reporter.protein,ProteinGroup,character-method Man page
reporterProteins Man page
reporterProteins,ProteinGroup-method Man page
reporter-specific Man page
REPORTERSPECIFIC Man page
reporterTagMasses Man page
reporterTagMasses,IBSpectra-method Man page
reporterTagNames Man page
reporterTagNames,IBSpectra-method Man page
sanitize Man page
sequence.coverage Man page
shared.ratios Man page
shared.ratios.sign Man page
show,IBSpectra-method Man page
show,NoiseModel-method Man page
show,ProteinGroup-method Man page
specificities Man page
SPECIFICITIES Man page
spectra.count Man page
spectra.count2 Man page
spectrumSel Man page
spectrumSel,IBSpectra,character,missing-method Man page
spectrumSel,IBSpectra,data.frame,missing-method Man page
spectrumSel,IBSpectra,matrix,missing-method Man page
spectrumSel,IBSpectra,missing,character-method Man page
spectrumSel,IBSpectra,missing,missing-method Man page
spectrumTitles Man page
spectrumTitles,IBSpectra-method Man page
spectrumToPeptide Man page
spectrumToPeptide,ProteinGroup-method Man page
stddev Man page
stddev,NoiseModel-method Man page
subsetIBSpectra Man page
subtractAdditiveNoise Man page
subtractAdditiveNoise,IBSpectra-method Man page
summarize.ratios Man page
summary.ProteinGroup Man page
testPdflatex Man page
testPerl Man page
tikz.proteingroup Man page
Tlsd Man page
Tlsd-class Man page
TlsParameter-class Man page
TMT10plexSpectra Man page
TMT10plexSpectra-class Man page
TMT2plexSpectra Man page
TMT2plexSpectra-class Man page
TMT6plexSpectra Man page
TMT6plexSpectra2 Man page
TMT6plexSpectra2-class Man page
TMT6plexSpectra-class Man page
TMTSpectra Man page
TMTSpectra-class Man page
transform_pepmodif Man page
twodistr.plot Man page
UnivariateDistribution-class Man page
unspecific Man page
UNSPECIFIC Man page
variance Man page
variance,NoiseModel,numeric,missing-method Man page
variance,NoiseModel,numeric,numeric-method Man page
VARMETADATA Man page
weightedMean Man page
weightedMean,numeric,numeric-method Man page
weightedVariance Man page
weightedVariance,numeric,numeric,missing-method Man page
weightedVariance,numeric,numeric,numeric-method Man page
writeData Man page
writeData,IBSpectra-method Man page
writeHscoreData Man page
writeIBSpectra Man page
writePhosphoRSInput Man page
write.tex.commands Man page
write.xls.report Man page

Files

isobar/BinaryFiles
isobar/DESCRIPTION
isobar/NAMESPACE
isobar/NEWS
isobar/R
isobar/R/IBSpectra-class.R isobar/R/IBSpectra-plots.R isobar/R/MSnSet-methods.R isobar/R/NoiseModel-class.R isobar/R/ProteinGroup-class.R isobar/R/Tlsd-class.R isobar/R/distr-methods.R isobar/R/isobar-import.R isobar/R/metareport-utils.R isobar/R/ptm-methods.R isobar/R/ratio-methods.R isobar/R/report-utils-tex.R isobar/R/report-utils-xls.R isobar/R/report-utils.R isobar/R/sharedpep-methods.R isobar/R/utils.R isobar/R/zzz.R
isobar/README.md
isobar/build
isobar/build/vignette.rds
isobar/data
isobar/data/datalist
isobar/data/ib_phospho.rda
isobar/data/ibspiked_set1.rda
isobar/data/ibspiked_set2.rda
isobar/data/noise.model.hcd.rda
isobar/inst
isobar/inst/CITATION
isobar/inst/doc
isobar/inst/doc/isobar-devel.R
isobar/inst/doc/isobar-devel.Rnw
isobar/inst/doc/isobar-devel.pdf
isobar/inst/doc/isobar-ptm.R
isobar/inst/doc/isobar-ptm.Rnw
isobar/inst/doc/isobar-ptm.pdf
isobar/inst/doc/isobar-usecases.R
isobar/inst/doc/isobar-usecases.Rnw
isobar/inst/doc/isobar-usecases.pdf
isobar/inst/doc/isobar.R
isobar/inst/doc/isobar.Rnw
isobar/inst/doc/isobar.pdf
isobar/inst/pl
isobar/inst/pl/mascotParser.ini
isobar/inst/pl/mascotParser2.pl
isobar/inst/pl/mascotParserDelta_defunct.pl
isobar/inst/pl/modifconv.csv
isobar/inst/pl/msgfpParser.R
isobar/inst/pl/parsersConfig.xml
isobar/inst/pl/pidresParser.ini
isobar/inst/pl/pidresParser2.pl
isobar/inst/pl/psx2tab2.pl
isobar/inst/pl/tab2psx.pl
isobar/inst/pl/tab2xls.pl
isobar/inst/pl/tab2xlsx.pl
isobar/inst/report
isobar/inst/report/create_ibspectra.R
isobar/inst/report/create_meta_report.R
isobar/inst/report/create_proteingroup.R
isobar/inst/report/create_reports.R
isobar/inst/report/isobar-analysis.Rnw
isobar/inst/report/isobar-qc.Rnw
isobar/inst/report/meta-properties.R
isobar/inst/report/properties.R
isobar/inst/report/report-utils.tex
isobar/man
isobar/man/IBSpectra-class.Rd isobar/man/NoiseModel-class.Rd isobar/man/ProteinGroup-class.Rd isobar/man/TlsParameter-class.Rd isobar/man/Tlsd-class.Rd isobar/man/calc.delta.score.Rd isobar/man/calc.startpos.Rd isobar/man/calculate-pvalues.Rd isobar/man/calculate.dNSAF.Rd isobar/man/calculate.emPAI.Rd isobar/man/correct.peptide.ratios.Rd isobar/man/distr-methods.Rd isobar/man/fit-distr.Rd isobar/man/getPeptideModifContext.Rd isobar/man/getPhosphoRSProbabilities.Rd isobar/man/getPtmInfo.Rd isobar/man/groupMemberPeptides.Rd isobar/man/human.protein.names.Rd isobar/man/isobar-analysis.Rd isobar/man/isobar-data.Rd isobar/man/isobar-import.Rd isobar/man/isobar-log.Rd isobar/man/isobar-package.Rd isobar/man/isobar-plots.Rd isobar/man/isobar-preprocessing.Rd isobar/man/isobar-reports.Rd isobar/man/maplot.protein.Rd isobar/man/number.ranges.Rd isobar/man/observedKnownSites.Rd isobar/man/peptide.count.Rd isobar/man/proteinInfo-methods.Rd isobar/man/proteinNameAndDescription.Rd isobar/man/ratio-summ.Rd isobar/man/ratiosReshapeWide.Rd isobar/man/reporter.protein-methods.Rd isobar/man/sanitize.Rd isobar/man/shared.ratios.Rd isobar/man/shared.ratios.sign.Rd isobar/man/specificities.Rd isobar/man/spectra.count2.Rd isobar/man/subsetIBSpectra.Rd isobar/man/utils.Rd isobar/man/writeHscoreData.Rd isobar/man/writeIBSpectra.Rd
isobar/vignettes
isobar/vignettes/isobar-devel.Rnw
isobar/vignettes/isobar-ptm.Rnw
isobar/vignettes/isobar-usecases.Rnw
isobar/vignettes/isobar.Rnw
isobar/vignettes/isobar_lib.bib

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