isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

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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.

Author
Florian 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 publication
None
Maintainer
Florian P Breitwieser <florian.bw@gmail.com>
License
LGPL-2
Version
1.20.0
URLs

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...

Files in this package

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