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

In fbreitwieser/isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description

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.

Details

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)

Author(s)

Florian P Breitwieser <[e-mail]> and Jacques Colinge <[e-mail]>, with contributions from Xavier Robin <[e-mail]>

Maintainer: Florian P Breitwieser <[e-mail]>

fbreitwieser/isobar documentation built on May 16, 2019, 12:01 p.m.