This is the development version of SWATH2stats; for the stable release version, see SWATH2stats.

Transform and Filter SWATH Data for Statistical Packages

Bioconductor version: Development (3.20)

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 bluewin.ch>

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


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

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

# The following initializes usage of Bioc devel


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 1.35.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL-3
Depends R (>= 2.10.0)
Imports data.table, reshape2, ggplot2, stats, grDevices, graphics, utils, biomaRt, methods
System Requirements
URL https://peterblattmann.github.io/SWATH2stats/
Bug Reports https://github.com/peterblattmann/SWATH2stats
See More
Suggests testthat, knitr, rmarkdown
Linking To
Enhances MSstats, PECA, aLFQ
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_1.35.0.tar.gz
Windows Binary SWATH2stats_1.35.0.zip
macOS Binary (x86_64) SWATH2stats_1.35.0.tgz
macOS Binary (arm64)
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