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...

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

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