SWATH2stats

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see SWATH2stats.

Transform and Filter SWATH Data for Statistical Packages


Bioconductor version: 3.7

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>

Citation (from within R, enter citation("SWATH2stats")):

Installation

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


if (!require("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")
SWATH2stats example script PDF R Script
SWATH2stats package Vignette PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, ExperimentalDesign, MassSpectrometry, Preprocessing, Proteomics, Software
Version 1.10.2
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL-3
Depends R (>= 2.10.0)
Imports data.table, reshape2, grid, ggplot2, stats, grDevices, graphics, utils
System Requirements
URL
See More
Suggests testthat, aLFQ, knitr, PECA
Linking To
Enhances imsbInfer, MSstats
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package SWATH2stats_1.10.2.tar.gz
Windows Binary SWATH2stats_1.10.2.zip
Mac OS X 10.11 (El Capitan) SWATH2stats_1.10.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/SWATH2stats
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SWATH2stats
Bioc Package Browser https://code.bioconductor.org/browse/SWATH2stats/
Package Short Url https://bioconductor.org/packages/SWATH2stats/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive