DOI: 10.18129/B9.bioc.SWATH2stats  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SWATH2stats.

Transform and Filter SWATH Data for Statistical Packages

Bioconductor version: 3.16

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 <blattmann at imsb.biol.ethz.ch>

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


To install this package, start R (version "4.2") 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:



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 1.28.0
In Bioconductor since BioC 3.2 (R-3.2) (7.5 years)
License GPL-3
Depends R (>= 2.10.0)
Imports data.table, reshape2, ggplot2, stats, grDevices, graphics, utils, biomaRt, methods
Suggests testthat, knitr, rmarkdown
Enhances MSstats, PECA, aLFQ
URL https://peterblattmann.github.io/SWATH2stats/
BugReports https://github.com/peterblattmann/SWATH2stats
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_1.28.0.tar.gz
Windows Binary SWATH2stats_1.28.0.zip
macOS Binary (x86_64) SWATH2stats_1.28.0.tgz
macOS Binary (arm64) SWATH2stats_1.28.0.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/
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