SWATH2stats specifications

Information


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
Requirements
R(>=2.10.0), stats, grid, graphics, utils, testthat, grDevices, ggplot2, data.table, knitr, reshape2, aLFQ, PECA
Maintained Yes

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Maintainer


  • person_outline Peter Blattmann <>

Publication for SWATH2stats

SWATH2stats in publications

 (4)
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 […]

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 […]

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

[…] 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 […]

PMCID: 5405564
PMID: 28473886
DOI: 10.1080/20013078.2017.1314073

[…] 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 […]


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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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