isobar
provides methods for preprocessing, normalization, and
report generation for the analysis of quantitative mass spectrometry
proteomics data labeled withOA isobaric tags, such as iTRAQ and TMT.
Package: | isobar |
Version: | 1.1.2 |
biocViews: | Proteomics, MassSpectrometray, Bioinformatics, MultipleComparisons, QualityControl |
Depends: | R (>= 2.9.0), Biobase, stats, methods, ggplot2 |
Imports: | distr, biomaRt |
Suggests: | MSnbase,XML |
LazyLoad: | yes |
License: | LGPL-2 |
URL: | http://bioinformatics.cemm.oeaw.ac.at |
Collate: | utils.R ProteinGroup-class.R IBSpectra-class.R NoiseModel-class.R ratio-methods.R sharedpep-methods.R MSnSet-methods.R zzz.R |
Index:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | IBSpectra-class IBSpectra objects
NoiseModel-class NoiseModel objects
ProteinGroup-class ProteinGroup objects
do.log Log functions for IBSpectra objects
fitCauchy Fit weighted and unweighted Cauchy and Normal
distributions
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 isobaric tag
Proteomics data
isobar-plots IBSpectra plots
isobar-preprocessing IBSpectra preprocessing
isobar-reports Isobar reports
maplot.protein MAplot for individual proteins
number.ranges Helper function to transform number lists to
ranges
proteinInfo-methods Methods for Function proteinInfo
proteinRatios protein and peptide ratios
sanitize Helper function for LaTeX export
shared.ratios Shared ratio calculation
shared.ratios.sign Plot and get significantly shared ratios.
|
Further information is available in the following vignettes:
isobar | Isobar Overview (source, pdf) |
isobar-devel | Isobar for developers (source, pdf) |
Florian P Breitwieser <fbreitwieser@cemm.oeaw.ac.at> and Jacques Colinge <jcolinge@cemm.oeaw.ac.at>, with contributions from Xavier Robin <xavier.robin@unige.ch>
Maintainer: Florian P Breitwieser <fbreitwieser@cemm.oeaw.ac.at>
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