SWATH2stats

DOI: 10.18129/B9.bioc.SWATH2stats    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see SWATH2stats.

Transform and Filter SWATH Data for Statistical Packages

Bioconductor version: 3.8

This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.

Author: Peter Blattmann, Moritz Heusel and Ruedi Aebersold

Maintainer: Peter Blattmann <blattmann at imsb.biol.ethz.ch>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SWATH2stats")

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("SWATH2stats")

 

PDF	R Script	SWATH2stats example script
PDF	R Script	SWATH2stats package Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, ExperimentalDesign, ImmunoOncology, MassSpectrometry, Preprocessing, Proteomics, Software
Version	1.12.1
In Bioconductor since	BioC 3.2 (R-3.2) (3.5 years)
License	GPL-3
Depends	R (>= 2.10.0)
Imports	data.table, reshape2, grid, ggplot2, stats, grDevices, graphics, utils, biomaRt
LinkingTo
Suggests	testthat, aLFQ, knitr, PECA
SystemRequirements
Enhances	imsbInfer, MSstats
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SWATH2stats_1.12.1.tar.gz
Windows Binary	SWATH2stats_1.12.1.zip
Mac OS X 10.11 (El Capitan)	SWATH2stats_1.12.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SWATH2stats
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SWATH2stats
Package Short Url	http://bioconductor.org/packages/SWATH2stats/
Package Downloads Report	Download Stats