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:
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) |