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Transform and Filter SWATH Data for Statistical Packages

Bioconductor version: Release (3.19)

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 [aut, cre] Moritz Heusel [aut] Ruedi Aebersold [aut]

Maintainer: Peter Blattmann <peter_blattmann at>

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


To install this package, start R (version "4.4") and enter:

if (!require("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:

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


biocViews Annotation, ExperimentalDesign, ImmunoOncology, MassSpectrometry, Preprocessing, Proteomics, Software
Version 1.34.0
In Bioconductor since BioC 3.2 (R-3.2) (9 years)
License GPL-3
Depends R (>= 2.10.0)
Imports data.table, reshape2, ggplot2, stats, grDevices, graphics, utils, biomaRt, methods
System Requirements
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Suggests testthat, knitr, rmarkdown
Linking To
Enhances MSstats, PECA, aLFQ
Depends On Me
Imports Me
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Package Archives

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

Source Package SWATH2stats_1.34.0.tar.gz
Windows Binary
macOS Binary (x86_64) SWATH2stats_1.34.0.tgz
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive