IPPD

DOI: 10.18129/B9.bioc.IPPD    

This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see IPPD.

Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching

Bioconductor version: Release (3.11)

The package provides functionality to extract isotopic peak patterns from raw mass spectra. This is done by fitting a large set of template basis functions to the raw spectrum using either nonnegative least squares or least absolute deviation fittting. The package offers a flexible function which tries to estimate model parameters in a way tailored to the peak shapes in the data. The package also provides functionality to process LCMS runs.

Author: Martin Slawski <ms at cs.uni-saarland.de>, Rene Hussong <rene.hussong at uni.lu>, Andreas Hildebrandt <andreas.hildebrandt at uni-mainz.de>, Matthias Hein <hein at cs.uni-saarland.de>

Maintainer: Martin Slawski <ms at cs.uni-saarland.de>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("IPPD")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("IPPD")

 

PDF	R Script	IPPD Manual
PDF		Reference Manual

Details

biocViews	Proteomics, Software
Version	1.35.0
In Bioconductor since	BioC 2.8 (R-2.13) (9.5 years)
License	GPL (version 2 or later)
Depends	R (>= 2.12.0), MASS, Matrix, XML, digest, bitops
Imports	methods, stats, graphics
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	RforProteomics
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	IPPD_1.35.0.tar.gz
Windows Binary	IPPD_1.35.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/IPPD
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IPPD
Package Short Url	https://bioconductor.org/packages/IPPD/
Package Downloads Report	Download Stats