Learn R Programming

⚠️There's a newer version (0.7.9) of this package.Take me there.

protViz (version 0.1.98)

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Description

This R package helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do solid data analysis for small scale data sets.

Copy Link

Version

Install

install.packages('protViz')

Monthly Downloads

444

Version

0.1.98

License

GPL-3

Maintainer

Christian Panse

Last Published

June 25th, 2014

Functions in protViz (0.1.98)

PTM_MarkerFinder

PTM MarkerFinder
genMod

Generates all possible modification of a given peptide seqence and modification pattern
averagine

averagine - a data set conatining isotope envelopes of averagine peptides
fetuinLFQ

fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods.
deisotoper

find isotop pattern in a given mass spectrum
msms

A data set containing tandem mass spectra of an LCMS experiment.
pgImporter

Progenesis Importer Function
lcmsmap

LC-MS Map
parentIonMass

Compute Parent Ion Mass of a Peptide Sequence
swath

swath library generator
iTRAQ

iTRAQ - A small 8-plex iTRAQ data set with confident identified peptides from 5 proteins.
de_novo

de-novo on tandem ms
massDeviationPlot

Mass Deviation Plot
HexNAc

HexNAc - Analysis of N-HexNAc glycopeptides by LC-MS/MS, using HCD and ETD fragmentation techniques
pgLFQfeature

pgLFQfeature - A data set with a featuremap export ProgenesisLCMS
peakplot

Labelling of Peptide Fragment Mass Spectra
pgLFQtNpq

Label Free Quantification using the top N peptide approach
pressureProfileSummary

A misc function for finding NN time slots in pressure profile data.
pressureProfilePlot

Plotting pressure profile data from Eksigent LC pumps
fragmentIon

Compute the b and y Fragment Ions of a Peptide Sequence
pgLFQprot

pgLFQprot - A data set with a featuremap export ProgenesisLCMS
iTRAQ2GroupAnalysis

iTRAQ two group analysis
findNN_

find index of nearest neighbor
findNN

find index of nearest neighbor
AA

AA - amino acid table
PTM_MarkerFinder_util

PTM MarkerFinder util plot
pressureProfile

NanoLC pressure profile
psm

compute a matching between a peptide sequence and a MS2 spectrum
iRTpeptides

iRT peptides - independent retention time peptides
pgLFQaov

iTRAQ two group analysis