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SWATH2stats specifications


Unique identifier OMICS_12615
Name SWATH2stats
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.10.2
Stability Stable
R(>=2.10.0), stats, grid, graphics, utils, testthat, grDevices, ggplot2, data.table, knitr, reshape2, aLFQ, PECA
Maintained Yes




No version available



  • person_outline Peter Blattmann

Publication for SWATH2stats

SWATH2stats citations


Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines

Cell Syst
PMCID: 5747350
PMID: 29226804
DOI: 10.1016/j.cels.2017.11.002

[…] after retention time alignment. For runs where no peak was identified the area was requantified using the single shortest Path method (). The data was then processed using the R/Bioconductor package SWATH2stats (). Precursors had to pass an m-score threshold of 1E-05 in at least 20% of the 291 files to be selected for further analysis. These threshold resulted in an estimated precursor FDR of 0.0 […]


Statistical control of peptide and protein error rates in large scale targeted DIA analyses

Nat Methods
PMCID: 5581544
PMID: 28825704
DOI: 10.1038/nmeth.4398

[…] on the peptide- and protein-levels. This can be achieved, for example, by adapting a target-decoy approach as initially implemented for protein-level spectrum-centric analyses in MAYU or recently in SWATH2stats. Another option is the application of non-parametric modeling strategies for computing posterior probabilities at the peptide- and protein-level, as have been adapted for DIA analyses in D […]


Enhanced differential expression statistics for data independent acquisition proteomics

Sci Rep
PMCID: 5517573
PMID: 28724900
DOI: 10.1038/s41598-017-05949-y

[…] from 72 monozygotic and 44 dizygotic twins. The preprocessed OpenSWATH data was downloaded from the PRIDE Archive (id PXD001064) and converted to suitable matrix format for statistical analysis using SWATH2stats R-package. The peptide-level data was median normalized and used as input for ROPECA, MSstats and mapDIA analysis. For t-test, we used the available protein-level data, which was median no […]


Unique molecular profile of exosomes derived from primary human proximal tubular epithelial cells under diseased conditions

J Extracell Vesicles
PMCID: 5405564
PMID: 28473886
DOI: 10.1080/20013078.2017.1314073

[…] R below 0.1% as previously described []. Feature alignment was performed using the transition of identification confidence algorithm (https://pypi.python.org/pypi/msproteomicstools) and the R package SWATH2stats [] was used to filter low scoring peak groups and remove proteins with less than two associated peptides. MSstats [] was used to generate differential expression values with an adjusted p- […]

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SWATH2stats institution(s)
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD program in Molecular and Translational Biomedicine, Competence Center Personalized Medicine UZH/ETH & Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland; UGent / VIB, BELGIUM
SWATH2stats funding source(s)
This work was supported by the Swiss SystemsX.ch initiative, evaluated by the Swiss National Science Foundation, by grants from the European research council [233226-PROTEOMICS v3.0] and the Institut Mérieux, by the Swiss National Science Foundation [3100A0-130530], Advanced ERC grant [#670821], ETH Zurich and SystemsX.ch.

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