DOI: 10.18129/B9.bioc.SWATH2stats    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see SWATH2stats.

Transform and Filter SWATH Data for Statistical Packages

Bioconductor version: 3.10

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")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


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


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



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


biocViews Annotation, ExperimentalDesign, ImmunoOncology, MassSpectrometry, Preprocessing, Proteomics, Software
Version 1.16.0
In Bioconductor since BioC 3.2 (R-3.2) (4.5 years)
License GPL-3
Depends R (>= 2.10.0)
Imports data.table, reshape2, grid, ggplot2, stats, grDevices, graphics, utils, biomaRt
Suggests testthat, knitr
Enhances imsbInfer, MSstats, PECA, aLFQ
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_1.16.0.tar.gz
Windows Binary SWATH2stats_1.16.0.zip
Mac OS X 10.11 (El Capitan) SWATH2stats_1.16.0.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 https://bioconductor.org/packages/SWATH2stats/
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